{
 "cells": [
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": [
    "# GO Annotation Analysis\n",
    "\n",
    "Analyzes the associations between genes and GO terms in the Gene Ontology (GO) database.\n",
    "\n",
    "In particular, categorizes associations based on:\n",
    "\n",
    "- whether they have been \"retracted\" (i.e., removed from the database)\n",
    "- whether they have been reviewed and accepted or rejected via IBA"
   ],
   "id": "e82528c7acc91898"
  },
  {
   "metadata": {
    "collapsed": true,
    "ExecuteTime": {
     "end_time": "2025-01-16T01:01:52.125658Z",
     "start_time": "2025-01-16T01:01:52.121736Z"
    }
   },
   "cell_type": "code",
   "source": [
    "import pandas as pd\n",
    "\n",
    "from tests.test_implementations.test_robot_template import adapter\n",
    "\n",
    "# a recent release plus an older one that may have retracted entries\n",
    "\n",
    "RELEASES = [\n",
    "    \"2024-11-03\",\n",
    "    \"2024-06-10\",\n",
    "    \"2020-01-01\",\n",
    "]\n",
    "\n",
    "LATEST = RELEASES[0]\n",
    "PREVIOUS = RELEASES[1:]\n",
    "assert all(r < LATEST for r in PREVIOUS)"
   ],
   "id": "initial_id",
   "outputs": [],
   "execution_count": 1
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T01:01:52.132069Z",
     "start_time": "2025-01-16T01:01:52.129698Z"
    }
   },
   "cell_type": "code",
   "source": "NEW_CUTOFF = \"2024-06-01\"",
   "id": "49978ca9b485fbb2",
   "outputs": [],
   "execution_count": 2
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T01:01:52.281969Z",
     "start_time": "2025-01-16T01:01:52.279065Z"
    }
   },
   "cell_type": "code",
   "source": [
    "# taxa to analyze\n",
    "\n",
    "TAXA = [\n",
    "    (\"human\", \"goa_human\", 9606),\n",
    "    (\"Arabidopsis thaliana\", \"tair\", 3702),\n",
    "    (\"yeast\", \"sgd\", 559292),\n",
    "]"
   ],
   "id": "6018e587719b9375",
   "outputs": [],
   "execution_count": 3
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T01:01:52.292074Z",
     "start_time": "2025-01-16T01:01:52.289520Z"
    }
   },
   "cell_type": "code",
   "source": "GAF_URL_TEMPLATE = \"https://release.geneontology.org/{date}/annotations/{name}.gaf.gz\"",
   "id": "7308ce91009184f6",
   "outputs": [],
   "execution_count": 4
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T01:01:54.402787Z",
     "start_time": "2025-01-16T01:01:52.338558Z"
    }
   },
   "cell_type": "code",
   "source": "from oaklib.datamodels.vocabulary import IS_A, PART_OF",
   "id": "e5d71d36e84b2d23",
   "outputs": [],
   "execution_count": 5
  },
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": "## Create an OAK adapter for the GO ontology",
   "id": "aa0baac1347bdbad"
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T01:02:10.701075Z",
     "start_time": "2025-01-16T01:01:54.406977Z"
    }
   },
   "cell_type": "code",
   "source": [
    "from oaklib import get_adapter\n",
    "\n",
    "go = get_adapter(\"sqlite:obo:go\")"
   ],
   "id": "5ec745bd2131923d",
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Downloading go.db.gz: 0.00B [00:00, ?B/s]"
      ],
      "application/vnd.jupyter.widget-view+json": {
       "version_major": 2,
       "version_minor": 0,
       "model_id": "aaf16a6ab071468590f8ec5a8690270e"
      }
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "execution_count": 6
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T01:02:11.205688Z",
     "start_time": "2025-01-16T01:02:10.709344Z"
    }
   },
   "cell_type": "code",
   "source": "obsoletes = set(go.obsoletes())",
   "id": "2639655a1230be36",
   "outputs": [],
   "execution_count": 7
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T01:02:11.219520Z",
     "start_time": "2025-01-16T01:02:11.217763Z"
    }
   },
   "cell_type": "code",
   "source": "",
   "id": "323074c9573b3799",
   "outputs": [],
   "execution_count": null
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T01:02:12.966565Z",
     "start_time": "2025-01-16T01:02:11.231132Z"
    }
   },
   "cell_type": "code",
   "source": "binding_terms = set(go.descendants(\"GO:0005488\", predicates=[IS_A]))",
   "id": "a75d36046527380e",
   "outputs": [],
   "execution_count": 8
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T01:02:13.187408Z",
     "start_time": "2025-01-16T01:02:12.977295Z"
    }
   },
   "cell_type": "code",
   "source": [
    "antislim_terms = set(go.subset_members(\"gocheck_do_not_annotate\")).union(go.subset_members(\"gocheck_obsoletion_candidate\"))\n",
    "non_informative = binding_terms.union(antislim_terms)\n"
   ],
   "id": "7c29df1790c1eaa",
   "outputs": [],
   "execution_count": 9
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T07:06:14.986685Z",
     "start_time": "2025-01-16T07:06:09.128386Z"
    }
   },
   "cell_type": "code",
   "source": [
    "mf_terms = set(go.descendants(\"GO:0003674\", predicates=[IS_A]))\n",
    "bp_terms = set(go.descendants(\"GO:0008150\", predicates=[IS_A]))\n",
    "cc_terms = set(go.descendants(\"GO:0005575\", predicates=[IS_A]))"
   ],
   "id": "ea09b5a5d4b41a41",
   "outputs": [],
   "execution_count": 96
  },
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": "## Load annotations from the archive",
   "id": "90bdc6b371566c7d"
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T01:02:13.215121Z",
     "start_time": "2025-01-16T01:02:13.212662Z"
    }
   },
   "cell_type": "code",
   "source": [
    "from oaklib.parsers import GafAssociationParser\n",
    "gaf_parser = GafAssociationParser()"
   ],
   "id": "1ff5c9430db09c",
   "outputs": [],
   "execution_count": 10
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T01:02:13.232733Z",
     "start_time": "2025-01-16T01:02:13.228Z"
    }
   },
   "cell_type": "code",
   "source": [
    "import requests_cache\n",
    "\n",
    "session = requests_cache.CachedSession(\n",
    "    cache_name='gaf_cache',\n",
    "    backend='sqlite',  # or 'memory' for in-memory cache\n",
    "    expire_after=24*60*60,  # Cache expiration in seconds\n",
    "    allowable_codes=[200],  # Only cache successful responses\n",
    ")"
   ],
   "id": "6a60e3aaac287013",
   "outputs": [],
   "execution_count": 11
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T01:02:19.564028Z",
     "start_time": "2025-01-16T01:02:19.559273Z"
    }
   },
   "cell_type": "code",
   "source": [
    "from oaklib.datamodels.association import ParserConfiguration, NegatedAssociation\n",
    "import io\n",
    "import gzip\n",
    "\n",
    "def get_gaf(release, name):\n",
    "    config = ParserConfiguration(preserve_negated_associations=True)\n",
    "    url = GAF_URL_TEMPLATE.format(date=release, name=name)\n",
    "    # open the URL as a file object using requests\n",
    "    with session.get(url, stream=True) as response:\n",
    "        # Decompress the gzipped content and create a text stream\n",
    "        decompressed = gzip.decompress(response.content)\n",
    "        text_stream = io.TextIOWrapper(io.BytesIO(decompressed))\n",
    "        print(f\"Reading {url} using {config}\")\n",
    "        return list(gaf_parser.parse(text_stream, configuration=config))"
   ],
   "id": "e094a1d0a870069f",
   "outputs": [],
   "execution_count": 12
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T01:02:40.209582Z",
     "start_time": "2025-01-16T01:02:40.207433Z"
    }
   },
   "cell_type": "code",
   "source": "",
   "id": "a17102634f83407",
   "outputs": [],
   "execution_count": null
  },
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": "## Load all annotations into a cache",
   "id": "1eb89218612607dd"
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T01:05:30.983720Z",
     "start_time": "2025-01-16T01:02:42.258853Z"
    }
   },
   "cell_type": "code",
   "source": [
    "from collections import defaultdict\n",
    "\n",
    "db = defaultdict(dict)\n",
    "for r in RELEASES:\n",
    "    for name, grp, tax_id in TAXA:\n",
    "        print(f\"Loading {r} {name}\")\n",
    "        assocs = get_gaf(r, grp)\n",
    "        print(f\"Loaded {len(assocs)} associations\")\n",
    "        neg_assocs = [x for x in assocs if x.negated]\n",
    "        print(f\"  {len(neg_assocs)} negated associations\")\n",
    "        db[grp][r] = assocs"
   ],
   "id": "d81f4578bced71a7",
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Loading 2024-11-03 human\n",
      "Reading https://release.geneontology.org/2024-11-03/annotations/goa_human.gaf.gz using ParserConfiguration(preserve_negated_associations=True, include_association_attributes=None, primary_knowledge_source=None, aggregator_knowledge_source=None)\n",
      "Loaded 782823 associations\n",
      "  1494 negated associations\n",
      "Loading 2024-11-03 Arabidopsis thaliana\n",
      "Reading https://release.geneontology.org/2024-11-03/annotations/tair.gaf.gz using ParserConfiguration(preserve_negated_associations=True, include_association_attributes=None, primary_knowledge_source=None, aggregator_knowledge_source=None)\n",
      "Loaded 235371 associations\n",
      "  1374 negated associations\n",
      "Loading 2024-11-03 yeast\n",
      "Reading https://release.geneontology.org/2024-11-03/annotations/sgd.gaf.gz using ParserConfiguration(preserve_negated_associations=True, include_association_attributes=None, primary_knowledge_source=None, aggregator_knowledge_source=None)\n",
      "Loaded 120823 associations\n",
      "  6 negated associations\n",
      "Loading 2024-06-10 human\n",
      "Reading https://release.geneontology.org/2024-06-10/annotations/goa_human.gaf.gz using ParserConfiguration(preserve_negated_associations=True, include_association_attributes=None, primary_knowledge_source=None, aggregator_knowledge_source=None)\n",
      "Loaded 707168 associations\n",
      "  1308 negated associations\n",
      "Loading 2024-06-10 Arabidopsis thaliana\n",
      "Reading https://release.geneontology.org/2024-06-10/annotations/tair.gaf.gz using ParserConfiguration(preserve_negated_associations=True, include_association_attributes=None, primary_knowledge_source=None, aggregator_knowledge_source=None)\n",
      "Loaded 235504 associations\n",
      "  1373 negated associations\n",
      "Loading 2024-06-10 yeast\n",
      "Reading https://release.geneontology.org/2024-06-10/annotations/sgd.gaf.gz using ParserConfiguration(preserve_negated_associations=True, include_association_attributes=None, primary_knowledge_source=None, aggregator_knowledge_source=None)\n",
      "Loaded 117290 associations\n",
      "  7 negated associations\n",
      "Loading 2020-01-01 human\n",
      "Reading https://release.geneontology.org/2020-01-01/annotations/goa_human.gaf.gz using ParserConfiguration(preserve_negated_associations=True, include_association_attributes=None, primary_knowledge_source=None, aggregator_knowledge_source=None)\n",
      "Loaded 495361 associations\n",
      "  1244 negated associations\n",
      "Loading 2020-01-01 Arabidopsis thaliana\n",
      "Reading https://release.geneontology.org/2020-01-01/annotations/tair.gaf.gz using ParserConfiguration(preserve_negated_associations=True, include_association_attributes=None, primary_knowledge_source=None, aggregator_knowledge_source=None)\n",
      "Loaded 236821 associations\n",
      "  1364 negated associations\n",
      "Loading 2020-01-01 yeast\n",
      "Reading https://release.geneontology.org/2020-01-01/annotations/sgd.gaf.gz using ParserConfiguration(preserve_negated_associations=True, include_association_attributes=None, primary_knowledge_source=None, aggregator_knowledge_source=None)\n",
      "Loaded 120916 associations\n",
      "  28 negated associations\n"
     ]
    }
   ],
   "execution_count": 13
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T01:05:31.064502Z",
     "start_time": "2025-01-16T01:05:31.055034Z"
    }
   },
   "cell_type": "code",
   "source": "db[\"goa_human\"][LATEST][0]",
   "id": "69f2c5dd1f8ff101",
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Association(subject='UniProtKB:A0A024RBG1', predicate='enables', object='GO:0003723', property_values=[], subject_label='NUDT4B', predicate_label=None, object_label=None, negated=None, publications=['GO_REF:0000043'], evidence_type='IEA', supporting_objects=[], primary_knowledge_source='infores:UniProt', aggregator_knowledge_source=None, subject_closure=[], subject_closure_label=[], object_closure=[], object_closure_label=[], comments=[])"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "execution_count": 14
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T01:05:47.777533Z",
     "start_time": "2025-01-16T01:05:47.546272Z"
    }
   },
   "cell_type": "code",
   "source": "len([x for x in db[\"goa_human\"][LATEST] if x.negated])",
   "id": "846c6083be22e228",
   "outputs": [
    {
     "data": {
      "text/plain": [
       "1494"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "execution_count": 15
  },
  {
   "metadata": {},
   "cell_type": "code",
   "outputs": [],
   "execution_count": null,
   "source": "# reload modules\n",
   "id": "f3648e6d2ebabe76"
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T02:04:51.451900Z",
     "start_time": "2025-01-16T02:04:42.035195Z"
    }
   },
   "cell_type": "code",
   "source": "%load_ext autoreload\n",
   "id": "4e24da22a5fb7756",
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The autoreload extension is already loaded. To reload it, use:\n",
      "  %reload_ext autoreload\n"
     ]
    }
   ],
   "execution_count": 30
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T03:00:50.738855Z",
     "start_time": "2025-01-16T03:00:50.712857Z"
    }
   },
   "cell_type": "code",
   "source": "%autoreload 0",
   "id": "6c73a0e816464015",
   "outputs": [],
   "execution_count": 53
  },
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": "## Diffs by terms",
   "id": "9bc1bc750a447e06"
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T02:05:08.920771Z",
     "start_time": "2025-01-16T02:05:08.917999Z"
    }
   },
   "cell_type": "code",
   "source": "",
   "id": "ec7960ee3ab0d9da",
   "outputs": [],
   "execution_count": null
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T02:05:40.040840Z",
     "start_time": "2025-01-16T02:05:39.993321Z"
    }
   },
   "cell_type": "code",
   "source": [
    "from oaklib.utilities.associations.association_differ import AssociationDiffer\n",
    "\n",
    "\n",
    "differ = AssociationDiffer(adapter=go)"
   ],
   "id": "a349de5baadc2204",
   "outputs": [],
   "execution_count": 32
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T02:05:40.073956Z",
     "start_time": "2025-01-16T02:05:40.049886Z"
    }
   },
   "cell_type": "code",
   "source": "cache = {}",
   "id": "f6e2c4e58aca3bde",
   "outputs": [],
   "execution_count": 33
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T03:37:40.874524Z",
     "start_time": "2025-01-16T03:37:40.870953Z"
    }
   },
   "cell_type": "code",
   "source": "len(db[\"goa_human\"].keys())",
   "id": "b9100eeaecc2d4a2",
   "outputs": [
    {
     "data": {
      "text/plain": [
       "3"
      ]
     },
     "execution_count": 73,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "execution_count": 73
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T03:38:07.798450Z",
     "start_time": "2025-01-16T03:38:07.794257Z"
    }
   },
   "cell_type": "code",
   "source": "list(db[\"goa_human\"].keys())",
   "id": "1d15de57619b4e7b",
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['2024-11-03', '2024-06-10', '2020-01-01']"
      ]
     },
     "execution_count": 74,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "execution_count": 74
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T06:51:21.735705Z",
     "start_time": "2025-01-16T06:51:13.328317Z"
    }
   },
   "cell_type": "code",
   "source": [
    "#ix = differ.changes_by_terms(db[\"goa_human\"][LATEST], db[\"goa_human\"][PREVIOUS[0]], min_num_entities_changes=10, cache={})\n",
    "grp = \"sgd\"\n",
    "ix = differ.changes_by_terms(db[grp][PREVIOUS[0]], db[grp][LATEST], min_num_entities_changes=2, cache={})\n"
   ],
   "id": "dea16c8833b92aaf",
   "outputs": [],
   "execution_count": 89
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T06:51:21.756133Z",
     "start_time": "2025-01-16T06:51:21.751127Z"
    }
   },
   "cell_type": "code",
   "source": "len(ix)",
   "id": "1295df44a5e49396",
   "outputs": [
    {
     "data": {
      "text/plain": [
       "847"
      ]
     },
     "execution_count": 90,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "execution_count": 90
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T06:51:38.169273Z",
     "start_time": "2025-01-16T06:51:38.161271Z"
    }
   },
   "cell_type": "code",
   "source": [
    "for k in list(ix.keys())[0:5]:\n",
    "    print(k, go.label(k))"
   ],
   "id": "c52a32e82439ffb2",
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GO:1904688 regulation of cytoplasmic translational initiation\n",
      "GO:0170039 proteinogenic amino acid metabolic process\n",
      "GO:0005980 glycogen catabolic process\n",
      "GO:0045937 positive regulation of phosphate metabolic process\n",
      "GO:0042762 regulation of sulfur metabolic process\n"
     ]
    }
   ],
   "execution_count": 91
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T06:51:54.175669Z",
     "start_time": "2025-01-16T06:51:54.171142Z"
    }
   },
   "cell_type": "code",
   "source": "pubmed_adapter = get_adapter(\"pubmed:\")",
   "id": "acf63844088ab185",
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:eutils._internal.queryservice:No NCBI API key provided; throttling to 3 requests/second; see https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/\n"
     ]
    }
   ],
   "execution_count": 92
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T06:52:10.167483Z",
     "start_time": "2025-01-16T06:52:10.164456Z"
    }
   },
   "cell_type": "code",
   "source": [
    "from functools import lru_cache\n",
    "\n",
    "\n",
    "@lru_cache\n",
    "def pub_date(pmid):\n",
    "    m = pubmed_adapter.entity_metadata_map(pmid)\n",
    "    if m:\n",
    "        return m.get(\"year\")\n"
   ],
   "id": "f6b5935b55ce15ca",
   "outputs": [],
   "execution_count": 93
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T08:38:03.124949Z",
     "start_time": "2025-01-16T08:38:03.114051Z"
    }
   },
   "cell_type": "code",
   "source": [
    "from typing import Optional\n",
    "from oaklib.utilities.associations.association_differ import TermComparison\n",
    "\n",
    "\n",
    "def score_term_comparison(term: str, ix: TermComparison, max_date_inclusive=None, max_genes=20) -> Optional[dict]:\n",
    "    \"\"\"\n",
    "    We are interested in genes for which all evidence was from previously known.\n",
    "    \n",
    "    :param term: \n",
    "    :param ix: \n",
    "    :return: \n",
    "    \"\"\"\n",
    "    #all_genes = set(ix.old_associations_by_entity.keys()).union(ix.new_associations_by_entity.keys())\n",
    "    #gene_diff = all_genes - set(ix.old_associations_by_entity.keys()).intersection(ix.new_associations_by_entity.keys())\n",
    "    if len(ix.new_associations_by_entity) > max_genes:\n",
    "        return None\n",
    "    new_genes = set(ix.new_associations_by_entity.keys()) - set(ix.old_associations_by_entity.keys())\n",
    "    gene_id_to_label_map = {}\n",
    "    for g, assocs in ix.new_associations_by_entity.items():\n",
    "        gene_id_to_label_map[g] = assocs[0].subject_label\n",
    "    for g, assocs in ix.old_associations_by_entity.items():\n",
    "        gene_id_to_label_map[g] = assocs[0].subject_label\n",
    "    filtered_new_genes = {}\n",
    "    for gene in new_genes:\n",
    "        all_before_cutoff = True\n",
    "        for a in ix.new_associations_by_entity[gene]:\n",
    "            pmids = [x for x in a.publications if x.startswith(\"PMID\")]\n",
    "            if max_date_inclusive is not None:\n",
    "                # print(f\"{term} {gene}, pmids={pmids}\")\n",
    "                if not pmids:\n",
    "                    all_before_cutoff = False\n",
    "                else:\n",
    "                    pmid = pmids[0]\n",
    "                    date = pub_date(pmid)\n",
    "                    if date is None or date > max_date_inclusive:\n",
    "                        all_before_cutoff = False\n",
    "        if all_before_cutoff:\n",
    "            filtered_new_genes[gene] = ix.new_associations_by_entity[gene]\n",
    "    #gene_id_diff = len(gene_diff)\n",
    "    term_lbl = go.label(term)\n",
    "    if term in mf_terms:\n",
    "        ann_pred = \"that are capable of\"\n",
    "    elif term in bp_terms:\n",
    "        ann_pred = \"involved in\"\n",
    "    elif term in cc_terms:\n",
    "        ann_pred = \"localized to\"\n",
    "    else:\n",
    "        return\n",
    "    def as_genes_list(amap):\n",
    "        return [gene_id_to_label_map[g] for g in amap]\n",
    "    def as_str_list(amap):\n",
    "        return [str(g) for g in amap]\n",
    "    case = {\n",
    "        \"input\": f\"List all genes {ann_pred} {term_lbl}\",\n",
    "        \"ideal\": \"; \".join(as_genes_list(ix.new_associations_by_entity)),\n",
    "        \"original_input\": {\n",
    "            \"term\": str(term),\n",
    "            \"genes_current\": as_str_list(ix.new_associations_by_entity),\n",
    "            \"genes_previous\": as_str_list(ix.old_associations_by_entity),\n",
    "            \"genes_added\": as_genes_list(new_genes),\n",
    "            \"genes_added_prior_to_cutoff\": as_genes_list(filtered_new_genes),\n",
    "            \"num_genes_added_prior_to_cutoff\": len(filtered_new_genes),\n",
    "            \"date_cutoff\": max_date_inclusive,\n",
    "        }\n",
    "    }\n",
    "    return case"
   ],
   "id": "8415d4ef59e1c228",
   "outputs": [],
   "execution_count": 110
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-16T08:38:20.387476Z",
     "start_time": "2025-01-16T08:38:20.116376Z"
    }
   },
   "cell_type": "code",
   "source": [
    "import yaml\n",
    "\n",
    "n = 0\n",
    "for k in list(ix.keys()):\n",
    "    lbl = go.label(k)\n",
    "    if \"regulation\" in lbl:\n",
    "        continue\n",
    "    if \"response to\" in lbl:\n",
    "        continue\n",
    "    case = score_term_comparison(k, ix[k], max_date_inclusive=\"2022\")\n",
    "    if not case:\n",
    "        continue\n",
    "    if case[\"original_input\"][\"num_genes_added_prior_to_cutoff\"] > 2:\n",
    "        print(yaml.dump(case, sort_keys=False))\n",
    "        n += 1\n",
    "    if n > 40:\n",
    "        break"
   ],
   "id": "af913da8d3c2a149",
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "input: List all genes localized to respiratory chain complex IV\n",
      "ideal: COX6; COX12; COX5B; COX9; COX5A; COX4; COX8; MTC3; COX13; COX7; COX1; COX2;\n",
      "  COX3; COX26; AI4; AI5_ALPHA; AI3\n",
      "original_input:\n",
      "  term: GO:0045277\n",
      "  genes_current:\n",
      "  - SGD:S000001093\n",
      "  - SGD:S000004028\n",
      "  - SGD:S000001373\n",
      "  - SGD:S000002225\n",
      "  - SGD:S000004997\n",
      "  - SGD:S000003155\n",
      "  - SGD:S000004387\n",
      "  - SGD:S000003195\n",
      "  - SGD:S000003159\n",
      "  - SGD:S000004869\n",
      "  - SGD:S000007260\n",
      "  - SGD:S000007281\n",
      "  - SGD:S000007283\n",
      "  - SGD:S000113555\n",
      "  - SGD:S000007264\n",
      "  - SGD:S000007265\n",
      "  - SGD:S000007263\n",
      "  genes_previous:\n",
      "  - SGD:S000004387\n",
      "  - SGD:S000004028\n",
      "  - SGD:S000004857\n",
      "  - SGD:S000007260\n",
      "  genes_added:\n",
      "  - COX26\n",
      "  - COX13\n",
      "  - AI4\n",
      "  - COX4\n",
      "  - COX9\n",
      "  - AI3\n",
      "  - MTC3\n",
      "  - COX6\n",
      "  - COX3\n",
      "  - AI5_ALPHA\n",
      "  - COX5A\n",
      "  - COX5B\n",
      "  - COX7\n",
      "  - COX2\n",
      "  genes_added_prior_to_cutoff:\n",
      "  - COX26\n",
      "  - COX9\n",
      "  - COX3\n",
      "  - COX7\n",
      "  - COX2\n",
      "  num_genes_added_prior_to_cutoff: 5\n",
      "  date_cutoff: '2022'\n",
      "\n",
      "input: List all genes localized to TTT Hsp90 cochaperone complex\n",
      "ideal: TTI2; RVB2; TRA1; TTI1; RVB1; ASA1; TEL2\n",
      "original_input:\n",
      "  term: GO:0110078\n",
      "  genes_current:\n",
      "  - SGD:S000003897\n",
      "  - SGD:S000006156\n",
      "  - SGD:S000001141\n",
      "  - SGD:S000001516\n",
      "  - SGD:S000002598\n",
      "  - SGD:S000006289\n",
      "  - SGD:S000003331\n",
      "  genes_previous:\n",
      "  - SGD:S000003897\n",
      "  genes_added:\n",
      "  - RVB1\n",
      "  - TEL2\n",
      "  - TTI1\n",
      "  - ASA1\n",
      "  - RVB2\n",
      "  - TRA1\n",
      "  genes_added_prior_to_cutoff:\n",
      "  - RVB1\n",
      "  - TEL2\n",
      "  - TTI1\n",
      "  - ASA1\n",
      "  - RVB2\n",
      "  - TRA1\n",
      "  num_genes_added_prior_to_cutoff: 6\n",
      "  date_cutoff: '2022'\n",
      "\n",
      "input: List all genes localized to respiratory chain complex III\n",
      "ideal: COR1; RIP1; QCR6; QCR8; QCR7; QCR9; QCR10; CYT1; QCR2; COB\n",
      "original_input:\n",
      "  term: GO:0045275\n",
      "  genes_current:\n",
      "  - SGD:S000000141\n",
      "  - SGD:S000000750\n",
      "  - SGD:S000001929\n",
      "  - SGD:S000003702\n",
      "  - SGD:S000002937\n",
      "  - SGD:S000003415\n",
      "  - SGD:S000003529\n",
      "  - SGD:S000005591\n",
      "  - SGD:S000006395\n",
      "  - SGD:S000007270\n",
      "  genes_previous:\n",
      "  - SGD:S000007270\n",
      "  genes_added:\n",
      "  - QCR10\n",
      "  - COR1\n",
      "  - CYT1\n",
      "  - QCR2\n",
      "  - QCR9\n",
      "  - QCR8\n",
      "  - QCR6\n",
      "  - QCR7\n",
      "  - RIP1\n",
      "  genes_added_prior_to_cutoff:\n",
      "  - QCR10\n",
      "  - COR1\n",
      "  - QCR2\n",
      "  num_genes_added_prior_to_cutoff: 3\n",
      "  date_cutoff: '2022'\n",
      "\n",
      "input: List all genes that are capable of alpha-1,4-glucosidase activity\n",
      "ideal: MAL62; MAL42; MAL22; MAL32; GTB1; MAL12; IMA1; IMA2; IMA3; IMA4; IMA5\n",
      "original_input:\n",
      "  term: GO:0004558\n",
      "  genes_current:\n",
      "  - SGD:S000029690\n",
      "  - SGD:S000029687\n",
      "  - SGD:S000029682\n",
      "  - SGD:S000000503\n",
      "  - SGD:S000002629\n",
      "  - SGD:S000003524\n",
      "  - SGD:S000003519\n",
      "  - SGD:S000005517\n",
      "  - SGD:S000001434\n",
      "  - SGD:S000003757\n",
      "  - SGD:S000003752\n",
      "  genes_previous:\n",
      "  - SGD:S000002629\n",
      "  genes_added:\n",
      "  - MAL42\n",
      "  - IMA1\n",
      "  - IMA3\n",
      "  - IMA4\n",
      "  - IMA5\n",
      "  - IMA2\n",
      "  - MAL22\n",
      "  - MAL32\n",
      "  - MAL62\n",
      "  - MAL12\n",
      "  genes_added_prior_to_cutoff:\n",
      "  - MAL42\n",
      "  - MAL22\n",
      "  - MAL62\n",
      "  num_genes_added_prior_to_cutoff: 3\n",
      "  date_cutoff: '2022'\n",
      "\n",
      "input: List all genes that are capable of G-quadruplex DNA binding\n",
      "ideal: RAP1; MGS1; SUB1; DNA2; NSR1; VID22; MSS116; XRS2; SLX9; PIF1; MRE11; DBP2;\n",
      "  RAD50; DED1; DBP1; RRM3\n",
      "original_input:\n",
      "  term: GO:0051880\n",
      "  genes_current:\n",
      "  - SGD:S000005160\n",
      "  - SGD:S000005162\n",
      "  - SGD:S000004642\n",
      "  - SGD:S000001207\n",
      "  - SGD:S000003391\n",
      "  - SGD:S000004365\n",
      "  - SGD:S000002602\n",
      "  - SGD:S000002777\n",
      "  - SGD:S000003313\n",
      "  - SGD:S000004526\n",
      "  - SGD:S000004837\n",
      "  - SGD:S000005056\n",
      "  - SGD:S000005194\n",
      "  - SGD:S000005730\n",
      "  - SGD:S000006040\n",
      "  - SGD:S000001073\n",
      "  genes_previous:\n",
      "  - SGD:S000004526\n",
      "  - SGD:S000005160\n",
      "  - SGD:S000005194\n",
      "  - SGD:S000004837\n",
      "  - SGD:S000002777\n",
      "  - SGD:S000005162\n",
      "  - SGD:S000004642\n",
      "  - SGD:S000001207\n",
      "  - SGD:S000003391\n",
      "  - SGD:S000003313\n",
      "  - SGD:S000001073\n",
      "  - SGD:S000004365\n",
      "  genes_added:\n",
      "  - DBP2\n",
      "  - MSS116\n",
      "  - DED1\n",
      "  - DBP1\n",
      "  genes_added_prior_to_cutoff:\n",
      "  - DBP2\n",
      "  - MSS116\n",
      "  - DED1\n",
      "  - DBP1\n",
      "  num_genes_added_prior_to_cutoff: 4\n",
      "  date_cutoff: '2022'\n",
      "\n",
      "input: List all genes that are capable of alpha-glucosidase activity\n",
      "ideal: MAL62; MAL42; MAL22; ROT2; MAL32; SGA1; IMA4; IMA3; GTB1; CWH41; MAL12; IMA1;\n",
      "  IMA5; GDB1; IMA2; YMR196W; STA1; CPX-417; SUC2\n",
      "original_input:\n",
      "  term: GO:0090599\n",
      "  genes_current:\n",
      "  - SGD:S000029690\n",
      "  - SGD:S000029687\n",
      "  - SGD:S000029682\n",
      "  - SGD:S000000433\n",
      "  - SGD:S000000503\n",
      "  - SGD:S000001361\n",
      "  - SGD:S000003757\n",
      "  - SGD:S000001434\n",
      "  - SGD:S000002629\n",
      "  - SGD:S000002995\n",
      "  - SGD:S000003524\n",
      "  - SGD:S000003519\n",
      "  - SGD:S000003752\n",
      "  - SGD:S000006388\n",
      "  - SGD:S000005517\n",
      "  - SGD:S000004809\n",
      "  - SGD:S000029522\n",
      "  - SGD:S000217621\n",
      "  - SGD:S000001424\n",
      "  genes_previous:\n",
      "  - SGD:S000001361\n",
      "  - SGD:S000001434\n",
      "  - SGD:S000003757\n",
      "  - SGD:S000000433\n",
      "  - SGD:S000000503\n",
      "  - SGD:S000003752\n",
      "  - SGD:S000002995\n",
      "  - SGD:S000003519\n",
      "  - SGD:S000003524\n",
      "  - SGD:S000002629\n",
      "  - SGD:S000006388\n",
      "  - SGD:S000005517\n",
      "  - SGD:S000004809\n",
      "  - SGD:S000029522\n",
      "  - SGD:S000217621\n",
      "  - SGD:S000001424\n",
      "  genes_added:\n",
      "  - MAL42\n",
      "  - MAL22\n",
      "  - MAL62\n",
      "  genes_added_prior_to_cutoff:\n",
      "  - MAL42\n",
      "  - MAL22\n",
      "  - MAL62\n",
      "  num_genes_added_prior_to_cutoff: 3\n",
      "  date_cutoff: '2022'\n",
      "\n"
     ]
    }
   ],
   "execution_count": 111
  },
  {
   "metadata": {},
   "cell_type": "code",
   "outputs": [],
   "execution_count": null,
   "source": "",
   "id": "e56adcfa23306224"
  },
  {
   "metadata": {},
   "cell_type": "code",
   "outputs": [],
   "execution_count": null,
   "source": "",
   "id": "2a6846e7f9900ffd"
  },
  {
   "metadata": {},
   "cell_type": "code",
   "outputs": [],
   "execution_count": null,
   "source": "",
   "id": "bd2bfcfb2ee8ba69"
  },
  {
   "metadata": {},
   "cell_type": "code",
   "outputs": [],
   "execution_count": null,
   "source": "",
   "id": "bb928d0ff338adff"
  },
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": "## OLD ANALYSIS BELOW",
   "id": "8103fbec8c035bf5"
  },
  {
   "metadata": {},
   "cell_type": "code",
   "outputs": [],
   "execution_count": null,
   "source": "",
   "id": "f06ea434d4133a25"
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:24:34.655429Z",
     "start_time": "2025-01-06T01:24:34.650696Z"
    }
   },
   "cell_type": "code",
   "source": [
    "from functools import lru_cache\n",
    "\n",
    "\n",
    "\n",
    "@lru_cache\n",
    "def lineage(t: str):\n",
    "    up = set(go.ancestors(t, predicates=[IS_A, PART_OF], reflexive=True))\n",
    "    dn = set(go.descendants(t, predicates=[IS_A, PART_OF]))\n",
    "    return up.union(dn)\n",
    "\n",
    "#len(lineage(\"GO:0005737\"))\n",
    "\n",
    "@lru_cache\n",
    "def ancs(t: str):\n",
    "    return set(go.ancestors(t, predicates=[IS_A, PART_OF], reflexive=True))\n",
    "    "
   ],
   "id": "899161951deb3a20",
   "outputs": [],
   "execution_count": 289
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:24:48.377611Z",
     "start_time": "2025-01-06T01:24:48.370515Z"
    }
   },
   "cell_type": "code",
   "source": [
    "import pandas as pd\n",
    "\n",
    "def pmid(a):\n",
    "    pubs = [p for p in a.publications if p.startswith(\"PMID\")]\n",
    "    if pubs:\n",
    "        if len(pubs) > 1:\n",
    "            raise ValueError(f\"Multiple PMIDs: {pubs}\")\n",
    "        return pubs[0]\n",
    "    return None\n",
    "\n",
    "@lru_cache\n",
    "def lbl(t: str):\n",
    "    return go.label(t)\n",
    "\n",
    "def assocs_to_df(assocs: list, release: str):\n",
    "    \n",
    "    df = pd.DataFrame([{\n",
    "        \"subject\": a.subject,\n",
    "        \"subject_label\": a.subject_label,\n",
    "        \"predicate\": a.predicate,\n",
    "        \"object\": a.object,\n",
    "        \"object_label\": lbl(a.object),\n",
    "        \"object_obsoletes\": a.object in obsoletes,\n",
    "        \"object_uninformative\": a.object in non_informative,\n",
    "        \"object_closure\": ancs(a.object),\n",
    "        \"object_closure_redundant\": ancs(a.object) - {a.object},\n",
    "        \"evidence\": a.evidence_type,\n",
    "        \"is_iba\": a.evidence_type == \"IBA\",\n",
    "        \"negated\": a.negated,\n",
    "        \"pmid\": pmid(a),\n",
    "        \"pubs\": a.publications,\n",
    "        \"release\": release,\n",
    "    } for a in assocs])\n",
    "    return df"
   ],
   "id": "8aae919788e4f995",
   "outputs": [],
   "execution_count": 290
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:29:30.373325Z",
     "start_time": "2025-01-06T01:25:01.988051Z"
    }
   },
   "cell_type": "code",
   "source": [
    "human_df = assocs_to_df(db[\"goa_human\"][LATEST], LATEST)\n",
    "tair_df = assocs_to_df(db[\"tair\"][LATEST], LATEST)\n",
    "sgd_df = assocs_to_df(db[\"sgd\"][LATEST], LATEST)\n",
    "df = sgd_df"
   ],
   "id": "6a647db06b35a07",
   "outputs": [],
   "execution_count": 291
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:30:21.920341Z",
     "start_time": "2025-01-06T01:29:44.689297Z"
    }
   },
   "cell_type": "code",
   "source": "prev_df = assocs_to_df(db[\"sgd\"][PREVIOUS[-1]], PREVIOUS[-1])",
   "id": "c14a72ef574e29ce",
   "outputs": [],
   "execution_count": 292
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:30:36.207477Z",
     "start_time": "2025-01-06T01:30:36.191544Z"
    }
   },
   "cell_type": "code",
   "source": "df",
   "id": "2fbff3c4fea8f6b6",
   "outputs": [
    {
     "data": {
      "text/plain": [
       "               subject subject_label                   predicate      object  \\\n",
       "0       SGD:S000003381          GPC1  acts_upstream_of_or_within  GO:0090640   \n",
       "1       SGD:S000005701          ALE1  acts_upstream_of_or_within  GO:0090640   \n",
       "2       SGD:S000003381          GPC1  acts_upstream_of_or_within  GO:0036151   \n",
       "3       SGD:S000004492          RCF1  acts_upstream_of_or_within  GO:0033617   \n",
       "4       SGD:S000004977         SIW14                     enables  GO:0052845   \n",
       "...                ...           ...                         ...         ...   \n",
       "120818  SGD:S000003241          SEC9                 involved_in  GO:0006906   \n",
       "120819  SGD:S000004826          CEF1                     part_of  GO:0000974   \n",
       "120820  SGD:S000002551          MKC7                 involved_in  GO:0031505   \n",
       "120821  SGD:S000003008          HEM2                is_active_in  GO:0005829   \n",
       "120822  SGD:S000001122          LAM4                 involved_in  GO:0032366   \n",
       "\n",
       "                                             object_label  object_obsoletes  \\\n",
       "0       phosphatidylcholine biosynthesis from sn-glyce...             False   \n",
       "1       phosphatidylcholine biosynthesis from sn-glyce...             False   \n",
       "2               phosphatidylcholine acyl-chain remodeling             False   \n",
       "3             mitochondrial cytochrome c oxidase assembly             False   \n",
       "4       inositol-5-diphosphate-1,2,3,4,6-pentakisphosp...             False   \n",
       "...                                                   ...               ...   \n",
       "120818                                     vesicle fusion             False   \n",
       "120819                                      Prp19 complex             False   \n",
       "120820                 fungal-type cell wall organization             False   \n",
       "120821                                            cytosol             False   \n",
       "120822                     intracellular sterol transport             False   \n",
       "\n",
       "        object_uninformative  \\\n",
       "0                      False   \n",
       "1                      False   \n",
       "2                      False   \n",
       "3                      False   \n",
       "4                      False   \n",
       "...                      ...   \n",
       "120818                 False   \n",
       "120819                 False   \n",
       "120820                 False   \n",
       "120821                 False   \n",
       "120822                 False   \n",
       "\n",
       "                                           object_closure  \\\n",
       "0       {GO:0019637, GO:0008152, BFO:0000015, GO:00066...   \n",
       "1       {GO:0019637, GO:0008152, BFO:0000015, GO:00066...   \n",
       "2       {GO:0019637, GO:0008152, GO:0006796, BFO:00000...   \n",
       "3       {GO:0043933, GO:0044085, GO:0065003, GO:001604...   \n",
       "4       {GO:0016817, GO:0016818, GO:0052842, GO:000382...   \n",
       "...                                                   ...   \n",
       "120818  {GO:0048284, GO:0051234, GO:0090174, GO:001604...   \n",
       "120819  {GO:0000974, BFO:0000004, BFO:0000040, BFO:000...   \n",
       "120820  {GO:0071554, GO:0016043, GO:0045229, GO:003150...   \n",
       "120821  {CARO:0030000, UBERON:0000061, CARO:0000003, G...   \n",
       "120822  {GO:0006869, GO:0015850, GO:0032365, GO:005123...   \n",
       "\n",
       "                                 object_closure_redundant evidence  is_iba  \\\n",
       "0       {GO:0019637, GO:0008152, GO:0006796, BFO:00000...      IGI   False   \n",
       "1       {GO:0019637, GO:0008152, GO:0006796, BFO:00000...      IGI   False   \n",
       "2       {GO:0019637, GO:0008152, GO:0006796, BFO:00000...      IMP   False   \n",
       "3       {GO:0043933, GO:0044085, GO:0022607, GO:007184...      IMP   False   \n",
       "4       {GO:0016817, GO:0016818, GO:0052842, GO:000382...      IDA   False   \n",
       "...                                                   ...      ...     ...   \n",
       "120818  {GO:0061024, BFO:0000015, GO:0009987, GO:00160...      IBA    True   \n",
       "120819  {BFO:0000004, BFO:0000040, BFO:0000002, GO:003...      IBA    True   \n",
       "120820  {GO:0071554, GO:0016043, GO:0045229, GO:000998...      IBA    True   \n",
       "120821  {CARO:0030000, CARO:0000000, BFO:0000004, GO:0...      IBA    True   \n",
       "120822  {GO:0032365, GO:0015918, GO:0051649, GO:000998...      IBA    True   \n",
       "\n",
       "       negated           pmid              pubs     release  \n",
       "0         None  PMID:30514764   [PMID:30514764]  2024-11-03  \n",
       "1         None  PMID:30514764   [PMID:30514764]  2024-11-03  \n",
       "2         None  PMID:30514764   [PMID:30514764]  2024-11-03  \n",
       "3         None  PMID:29746825   [PMID:29746825]  2024-11-03  \n",
       "4         None  PMID:26828065   [PMID:26828065]  2024-11-03  \n",
       "...        ...            ...               ...         ...  \n",
       "120818    None           None  [GO_REF:0000033]  2024-11-03  \n",
       "120819    None           None  [GO_REF:0000033]  2024-11-03  \n",
       "120820    None           None  [GO_REF:0000033]  2024-11-03  \n",
       "120821    None           None  [GO_REF:0000033]  2024-11-03  \n",
       "120822    None           None  [GO_REF:0000033]  2024-11-03  \n",
       "\n",
       "[120823 rows x 15 columns]"
      ],
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>subject</th>\n",
       "      <th>subject_label</th>\n",
       "      <th>predicate</th>\n",
       "      <th>object</th>\n",
       "      <th>object_label</th>\n",
       "      <th>object_obsoletes</th>\n",
       "      <th>object_uninformative</th>\n",
       "      <th>object_closure</th>\n",
       "      <th>object_closure_redundant</th>\n",
       "      <th>evidence</th>\n",
       "      <th>is_iba</th>\n",
       "      <th>negated</th>\n",
       "      <th>pmid</th>\n",
       "      <th>pubs</th>\n",
       "      <th>release</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>SGD:S000003381</td>\n",
       "      <td>GPC1</td>\n",
       "      <td>acts_upstream_of_or_within</td>\n",
       "      <td>GO:0090640</td>\n",
       "      <td>phosphatidylcholine biosynthesis from sn-glyce...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0019637, GO:0008152, BFO:0000015, GO:00066...</td>\n",
       "      <td>{GO:0019637, GO:0008152, GO:0006796, BFO:00000...</td>\n",
       "      <td>IGI</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:30514764</td>\n",
       "      <td>[PMID:30514764]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>SGD:S000005701</td>\n",
       "      <td>ALE1</td>\n",
       "      <td>acts_upstream_of_or_within</td>\n",
       "      <td>GO:0090640</td>\n",
       "      <td>phosphatidylcholine biosynthesis from sn-glyce...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0019637, GO:0008152, BFO:0000015, GO:00066...</td>\n",
       "      <td>{GO:0019637, GO:0008152, GO:0006796, BFO:00000...</td>\n",
       "      <td>IGI</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:30514764</td>\n",
       "      <td>[PMID:30514764]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>SGD:S000003381</td>\n",
       "      <td>GPC1</td>\n",
       "      <td>acts_upstream_of_or_within</td>\n",
       "      <td>GO:0036151</td>\n",
       "      <td>phosphatidylcholine acyl-chain remodeling</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0019637, GO:0008152, GO:0006796, BFO:00000...</td>\n",
       "      <td>{GO:0019637, GO:0008152, GO:0006796, BFO:00000...</td>\n",
       "      <td>IMP</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:30514764</td>\n",
       "      <td>[PMID:30514764]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>SGD:S000004492</td>\n",
       "      <td>RCF1</td>\n",
       "      <td>acts_upstream_of_or_within</td>\n",
       "      <td>GO:0033617</td>\n",
       "      <td>mitochondrial cytochrome c oxidase assembly</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0043933, GO:0044085, GO:0065003, GO:001604...</td>\n",
       "      <td>{GO:0043933, GO:0044085, GO:0022607, GO:007184...</td>\n",
       "      <td>IMP</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:29746825</td>\n",
       "      <td>[PMID:29746825]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>SGD:S000004977</td>\n",
       "      <td>SIW14</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:0052845</td>\n",
       "      <td>inositol-5-diphosphate-1,2,3,4,6-pentakisphosp...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0016817, GO:0016818, GO:0052842, GO:000382...</td>\n",
       "      <td>{GO:0016817, GO:0016818, GO:0052842, GO:000382...</td>\n",
       "      <td>IDA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:26828065</td>\n",
       "      <td>[PMID:26828065]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>120818</th>\n",
       "      <td>SGD:S000003241</td>\n",
       "      <td>SEC9</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0006906</td>\n",
       "      <td>vesicle fusion</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0048284, GO:0051234, GO:0090174, GO:001604...</td>\n",
       "      <td>{GO:0061024, BFO:0000015, GO:0009987, GO:00160...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>True</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>120819</th>\n",
       "      <td>SGD:S000004826</td>\n",
       "      <td>CEF1</td>\n",
       "      <td>part_of</td>\n",
       "      <td>GO:0000974</td>\n",
       "      <td>Prp19 complex</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0000974, BFO:0000004, BFO:0000040, BFO:000...</td>\n",
       "      <td>{BFO:0000004, BFO:0000040, BFO:0000002, GO:003...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>True</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>120820</th>\n",
       "      <td>SGD:S000002551</td>\n",
       "      <td>MKC7</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0031505</td>\n",
       "      <td>fungal-type cell wall organization</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0071554, GO:0016043, GO:0045229, GO:003150...</td>\n",
       "      <td>{GO:0071554, GO:0016043, GO:0045229, GO:000998...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>True</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>120821</th>\n",
       "      <td>SGD:S000003008</td>\n",
       "      <td>HEM2</td>\n",
       "      <td>is_active_in</td>\n",
       "      <td>GO:0005829</td>\n",
       "      <td>cytosol</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{CARO:0030000, UBERON:0000061, CARO:0000003, G...</td>\n",
       "      <td>{CARO:0030000, CARO:0000000, BFO:0000004, GO:0...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>True</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>120822</th>\n",
       "      <td>SGD:S000001122</td>\n",
       "      <td>LAM4</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0032366</td>\n",
       "      <td>intracellular sterol transport</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0006869, GO:0015850, GO:0032365, GO:005123...</td>\n",
       "      <td>{GO:0032365, GO:0015918, GO:0051649, GO:000998...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>True</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>120823 rows × 15 columns</p>\n",
       "</div>"
      ]
     },
     "execution_count": 293,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "execution_count": 293
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:30:50.059359Z",
     "start_time": "2025-01-06T01:30:50.054865Z"
    }
   },
   "cell_type": "code",
   "source": [
    "from typing import Dict, List, Optional\n",
    "\n",
    "\n",
    "def repair_assocs_df(assocs: pd.DataFrame):\n",
    "    \"\"\"\n",
    "    Ensures that IDs are normalized.\n",
    "    \n",
    "    :param assocs: \n",
    "    :return: \n",
    "    \"\"\"\n",
    "    # may not be 1:1\n",
    "    subject_label_to_ids: Dict[str, List[str]]\n",
    "    subject_label_to_ids = assocs.groupby(\"subject_label\")[\"subject\"].aggregate(lambda x: list(set(x))).to_dict()\n",
    "    labels_with_multiple_ids = {k: v for k, v in subject_label_to_ids.items() if len(v) > 1}\n",
    "    if labels_with_multiple_ids:\n",
    "        print(f\"Multiple IDs for {len(labels_with_multiple_ids)} labels\")\n",
    "        print(list(labels_with_multiple_ids.items())[:5])\n",
    "    labels_to_canonical = {k: sorted(list(v))[0] for k, v in subject_label_to_ids.items()}\n",
    "    assocs['subject'] = assocs['subject_label'].map(labels_to_canonical)\n",
    "    \n",
    "    "
   ],
   "id": "562804d220d9bd23",
   "outputs": [],
   "execution_count": 294
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:30:50.956550Z",
     "start_time": "2025-01-06T01:30:50.106919Z"
    }
   },
   "cell_type": "code",
   "source": [
    "test_df = tair_df.copy()\n",
    "repair_assocs_df(test_df)\n",
    "test_df"
   ],
   "id": "5ce16104b3c731e6",
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Multiple IDs for 5258 labels\n",
      "[('4CL1', ['TAIR:locus:2017602', 'AGI_LocusCode:AT1G51680']), ('4CL2', ['TAIR:locus:2094716', 'AGI_LocusCode:AT3G21240']), ('4CL3', ['TAIR:locus:2015003', 'AGI_LocusCode:AT1G65060']), ('AAC1', ['TAIR:locus:2077778', 'AGI_LocusCode:AT3G08580']), ('AAC2', ['AGI_LocusCode:AT5G13490', 'TAIR:locus:2185041'])]\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "                        subject subject_label     predicate      object  \\\n",
       "0       AGI_LocusCode:AT1G11880     AT1G11880       enables  GO:0000009   \n",
       "1       AGI_LocusCode:AT1G80420       ATXRCC1   involved_in  GO:0000012   \n",
       "2       AGI_LocusCode:AT1G74030          ENO1       part_of  GO:0000015   \n",
       "3       AGI_LocusCode:AT2G29560          ENOC       part_of  GO:0000015   \n",
       "4       AGI_LocusCode:AT2G36530          LOS2       part_of  GO:0000015   \n",
       "...                         ...           ...           ...         ...   \n",
       "235366       TAIR:locus:2058630     At2g23210       enables  GO:0010294   \n",
       "235367  AGI_LocusCode:AT2G15820         OTP51   involved_in  GO:0045292   \n",
       "235368       TAIR:locus:2143196     At5g15750   involved_in  GO:0042274   \n",
       "235369  AGI_LocusCode:AT4G14730          LFG1  is_active_in  GO:0016020   \n",
       "235370       TAIR:locus:2116525          SD25       enables  GO:0004672   \n",
       "\n",
       "                                      object_label  object_obsoletes  \\\n",
       "0           alpha-1,6-mannosyltransferase activity             False   \n",
       "1                       single strand break repair             False   \n",
       "2                phosphopyruvate hydratase complex             False   \n",
       "3                phosphopyruvate hydratase complex             False   \n",
       "4                phosphopyruvate hydratase complex             False   \n",
       "...                                            ...               ...   \n",
       "235366  abscisic acid glucosyltransferase activity             False   \n",
       "235367          mRNA cis splicing, via spliceosome             False   \n",
       "235368          ribosomal small subunit biogenesis             False   \n",
       "235369                                    membrane             False   \n",
       "235370                     protein kinase activity             False   \n",
       "\n",
       "        object_uninformative  \\\n",
       "0                      False   \n",
       "1                      False   \n",
       "2                      False   \n",
       "3                      False   \n",
       "4                      False   \n",
       "...                      ...   \n",
       "235366                 False   \n",
       "235367                 False   \n",
       "235368                 False   \n",
       "235369                 False   \n",
       "235370                 False   \n",
       "\n",
       "                                           object_closure  \\\n",
       "0       {GO:0000030, GO:0003824, GO:0016740, BFO:00000...   \n",
       "1       {GO:0043170, GO:0033554, GO:0008152, GO:000613...   \n",
       "2       {GO:0005829, GO:0110165, BFO:0000002, GO:00329...   \n",
       "3       {GO:0005829, GO:0110165, BFO:0000002, GO:00329...   \n",
       "4       {GO:0005829, GO:0110165, BFO:0000002, GO:00329...   \n",
       "...                                                   ...   \n",
       "235366  {GO:0035251, GO:0003824, GO:0016740, BFO:00000...   \n",
       "235367  {GO:0006397, GO:0008152, GO:0000375, BFO:00000...   \n",
       "235368  {GO:0042274, GO:0044085, GO:0009987, BFO:00000...   \n",
       "235369  {CARO:0030000, UBERON:0000061, CARO:0000003, G...   \n",
       "235370  {GO:0140096, GO:0003824, GO:0016740, BFO:00000...   \n",
       "\n",
       "                                 object_closure_redundant evidence  is_iba  \\\n",
       "0       {GO:0000030, GO:0003824, GO:0016740, BFO:00000...      IEA   False   \n",
       "1       {GO:0043170, GO:0008152, BFO:0000015, GO:00099...      IEA   False   \n",
       "2       {CARO:0030000, GO:0005829, BFO:0000004, CARO:0...      IEA   False   \n",
       "3       {CARO:0030000, GO:0005829, BFO:0000004, CARO:0...      IEA   False   \n",
       "4       {CARO:0030000, GO:0005829, BFO:0000004, CARO:0...      IEA   False   \n",
       "...                                                   ...      ...     ...   \n",
       "235366  {GO:0035251, GO:0003824, GO:0016740, BFO:00000...      IBA    True   \n",
       "235367  {GO:0009059, GO:0043170, GO:0006397, GO:000815...      IBA    True   \n",
       "235368  {GO:0044085, GO:0009987, BFO:0000015, GO:00226...      IBA    True   \n",
       "235369  {CARO:0030000, UBERON:0000061, CARO:0000003, G...      IBA    True   \n",
       "235370  {GO:0140096, GO:0003824, GO:0016740, BFO:00000...      IBA    True   \n",
       "\n",
       "       negated  pmid                                pubs     release  \n",
       "0         None  None  [TAIR:AnalysisReference:501756966]  2024-11-03  \n",
       "1         None  None  [TAIR:AnalysisReference:501756966]  2024-11-03  \n",
       "2         None  None  [TAIR:AnalysisReference:501756966]  2024-11-03  \n",
       "3         None  None  [TAIR:AnalysisReference:501756966]  2024-11-03  \n",
       "4         None  None  [TAIR:AnalysisReference:501756966]  2024-11-03  \n",
       "...        ...   ...                                 ...         ...  \n",
       "235366    None  None                    [GO_REF:0000033]  2024-11-03  \n",
       "235367    None  None                    [GO_REF:0000033]  2024-11-03  \n",
       "235368    None  None                    [GO_REF:0000033]  2024-11-03  \n",
       "235369    None  None                    [GO_REF:0000033]  2024-11-03  \n",
       "235370    None  None                    [GO_REF:0000033]  2024-11-03  \n",
       "\n",
       "[235371 rows x 15 columns]"
      ],
      "text/html": [
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       "\n",
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       "\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>subject</th>\n",
       "      <th>subject_label</th>\n",
       "      <th>predicate</th>\n",
       "      <th>object</th>\n",
       "      <th>object_label</th>\n",
       "      <th>object_obsoletes</th>\n",
       "      <th>object_uninformative</th>\n",
       "      <th>object_closure</th>\n",
       "      <th>object_closure_redundant</th>\n",
       "      <th>evidence</th>\n",
       "      <th>is_iba</th>\n",
       "      <th>negated</th>\n",
       "      <th>pmid</th>\n",
       "      <th>pubs</th>\n",
       "      <th>release</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>AGI_LocusCode:AT1G11880</td>\n",
       "      <td>AT1G11880</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:0000009</td>\n",
       "      <td>alpha-1,6-mannosyltransferase activity</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0000030, GO:0003824, GO:0016740, BFO:00000...</td>\n",
       "      <td>{GO:0000030, GO:0003824, GO:0016740, BFO:00000...</td>\n",
       "      <td>IEA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[TAIR:AnalysisReference:501756966]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AGI_LocusCode:AT1G80420</td>\n",
       "      <td>ATXRCC1</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0000012</td>\n",
       "      <td>single strand break repair</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0043170, GO:0033554, GO:0008152, GO:000613...</td>\n",
       "      <td>{GO:0043170, GO:0008152, BFO:0000015, GO:00099...</td>\n",
       "      <td>IEA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[TAIR:AnalysisReference:501756966]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AGI_LocusCode:AT1G74030</td>\n",
       "      <td>ENO1</td>\n",
       "      <td>part_of</td>\n",
       "      <td>GO:0000015</td>\n",
       "      <td>phosphopyruvate hydratase complex</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0005829, GO:0110165, BFO:0000002, GO:00329...</td>\n",
       "      <td>{CARO:0030000, GO:0005829, BFO:0000004, CARO:0...</td>\n",
       "      <td>IEA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[TAIR:AnalysisReference:501756966]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>AGI_LocusCode:AT2G29560</td>\n",
       "      <td>ENOC</td>\n",
       "      <td>part_of</td>\n",
       "      <td>GO:0000015</td>\n",
       "      <td>phosphopyruvate hydratase complex</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0005829, GO:0110165, BFO:0000002, GO:00329...</td>\n",
       "      <td>{CARO:0030000, GO:0005829, BFO:0000004, CARO:0...</td>\n",
       "      <td>IEA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[TAIR:AnalysisReference:501756966]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>AGI_LocusCode:AT2G36530</td>\n",
       "      <td>LOS2</td>\n",
       "      <td>part_of</td>\n",
       "      <td>GO:0000015</td>\n",
       "      <td>phosphopyruvate hydratase complex</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0005829, GO:0110165, BFO:0000002, GO:00329...</td>\n",
       "      <td>{CARO:0030000, GO:0005829, BFO:0000004, CARO:0...</td>\n",
       "      <td>IEA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[TAIR:AnalysisReference:501756966]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>235366</th>\n",
       "      <td>TAIR:locus:2058630</td>\n",
       "      <td>At2g23210</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:0010294</td>\n",
       "      <td>abscisic acid glucosyltransferase activity</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0035251, GO:0003824, GO:0016740, BFO:00000...</td>\n",
       "      <td>{GO:0035251, GO:0003824, GO:0016740, BFO:00000...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>True</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>235367</th>\n",
       "      <td>AGI_LocusCode:AT2G15820</td>\n",
       "      <td>OTP51</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0045292</td>\n",
       "      <td>mRNA cis splicing, via spliceosome</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0006397, GO:0008152, GO:0000375, BFO:00000...</td>\n",
       "      <td>{GO:0009059, GO:0043170, GO:0006397, GO:000815...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>True</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>235368</th>\n",
       "      <td>TAIR:locus:2143196</td>\n",
       "      <td>At5g15750</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0042274</td>\n",
       "      <td>ribosomal small subunit biogenesis</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0042274, GO:0044085, GO:0009987, BFO:00000...</td>\n",
       "      <td>{GO:0044085, GO:0009987, BFO:0000015, GO:00226...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>True</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>235369</th>\n",
       "      <td>AGI_LocusCode:AT4G14730</td>\n",
       "      <td>LFG1</td>\n",
       "      <td>is_active_in</td>\n",
       "      <td>GO:0016020</td>\n",
       "      <td>membrane</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{CARO:0030000, UBERON:0000061, CARO:0000003, G...</td>\n",
       "      <td>{CARO:0030000, UBERON:0000061, CARO:0000003, G...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>True</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>235370</th>\n",
       "      <td>TAIR:locus:2116525</td>\n",
       "      <td>SD25</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:0004672</td>\n",
       "      <td>protein kinase activity</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0140096, GO:0003824, GO:0016740, BFO:00000...</td>\n",
       "      <td>{GO:0140096, GO:0003824, GO:0016740, BFO:00000...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>True</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>235371 rows × 15 columns</p>\n",
       "</div>"
      ]
     },
     "execution_count": 295,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "execution_count": 295
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:30:51.054962Z",
     "start_time": "2025-01-06T01:30:50.997657Z"
    }
   },
   "cell_type": "code",
   "source": "test_df[test_df['subject_label'] == \"GALT6\"]",
   "id": "cc2f1ce6ee035902",
   "outputs": [
    {
     "data": {
      "text/plain": [
       "                        subject subject_label                   predicate  \\\n",
       "56871   AGI_LocusCode:AT5G62620         GALT6                  located_in   \n",
       "56872   AGI_LocusCode:AT5G62620         GALT6                  located_in   \n",
       "61144   AGI_LocusCode:AT5G62620         GALT6                 involved_in   \n",
       "85487   AGI_LocusCode:AT5G62620         GALT6                     enables   \n",
       "165846  AGI_LocusCode:AT5G62620         GALT6                  located_in   \n",
       "165851  AGI_LocusCode:AT5G62620         GALT6                 involved_in   \n",
       "165856  AGI_LocusCode:AT5G62620         GALT6                 involved_in   \n",
       "165858  AGI_LocusCode:AT5G62620         GALT6  acts_upstream_of_or_within   \n",
       "165863  AGI_LocusCode:AT5G62620         GALT6  acts_upstream_of_or_within   \n",
       "165869  AGI_LocusCode:AT5G62620         GALT6                     enables   \n",
       "210076  AGI_LocusCode:AT5G62620         GALT6                     enables   \n",
       "217996  AGI_LocusCode:AT5G62620         GALT6                is_active_in   \n",
       "\n",
       "            object                                       object_label  \\\n",
       "56871   GO:0005794                                    Golgi apparatus   \n",
       "56872   GO:0005794                                    Golgi apparatus   \n",
       "61144   GO:0006486                              protein glycosylation   \n",
       "85487   GO:0030246                               carbohydrate binding   \n",
       "165846  GO:0005794                                    Golgi apparatus   \n",
       "165851  GO:0010405          arabinogalactan protein metabolic process   \n",
       "165856  GO:0018258  protein O-linked glycosylation via hydroxyproline   \n",
       "165858  GO:0048354  mucilage biosynthetic process involved in seed...   \n",
       "165863  GO:1900056             negative regulation of leaf senescence   \n",
       "165869  GO:1990714    hydroxyproline O-galactosyltransferase activity   \n",
       "210076  GO:1990714    hydroxyproline O-galactosyltransferase activity   \n",
       "217996  GO:0000139                                     Golgi membrane   \n",
       "\n",
       "        object_obsoletes  object_uninformative  \\\n",
       "56871              False                 False   \n",
       "56872              False                 False   \n",
       "61144              False                 False   \n",
       "85487              False                  True   \n",
       "165846             False                 False   \n",
       "165851             False                 False   \n",
       "165856             False                 False   \n",
       "165858             False                 False   \n",
       "165863             False                 False   \n",
       "165869             False                 False   \n",
       "210076             False                 False   \n",
       "217996             False                 False   \n",
       "\n",
       "                                           object_closure  \\\n",
       "56871   {GO:0110165, GO:0043231, BFO:0000002, GO:00057...   \n",
       "56872   {GO:0110165, GO:0043231, BFO:0000002, GO:00057...   \n",
       "61144   {GO:0008152, BFO:0000015, GO:0009100, GO:00434...   \n",
       "85487   {BFO:0000015, GO:0003674, GO:0005488, BFO:0000...   \n",
       "165846  {GO:0110165, GO:0043231, BFO:0000002, GO:00057...   \n",
       "165851  {GO:0043170, GO:0044036, GO:0010384, GO:007155...   \n",
       "165856  {GO:0006493, GO:0008152, BFO:0000015, GO:00091...   \n",
       "165858  {GO:0032501, GO:0008152, GO:0048359, BFO:00000...   \n",
       "165863  {GO:0065007, BFO:0000015, GO:1900055, GO:00485...   \n",
       "165869  {GO:0003824, GO:0016740, BFO:0000015, GO:00083...   \n",
       "210076  {GO:0003824, GO:0016740, BFO:0000015, GO:00083...   \n",
       "217996  {GO:0110165, GO:0043231, BFO:0000002, GO:00057...   \n",
       "\n",
       "                                 object_closure_redundant evidence  is_iba  \\\n",
       "56871   {CARO:0030000, CARO:0000000, BFO:0000004, GO:0...      ISM   False   \n",
       "56872   {CARO:0030000, CARO:0000000, BFO:0000004, GO:0...      ISM   False   \n",
       "61144   {GO:0009059, GO:0043170, GO:0070085, GO:000815...      IEA   False   \n",
       "85487   {GO:0003674, BFO:0000015, GO:0005488, BFO:0000...      IEA   False   \n",
       "165846  {CARO:0030000, CARO:0000000, BFO:0000004, GO:0...      IDA   False   \n",
       "165851  {GO:0043170, GO:0044036, GO:0071554, GO:000815...      IMP   False   \n",
       "165856  {GO:0009059, GO:0006493, GO:0043170, GO:007008...      IDA   False   \n",
       "165858  {GO:0032501, GO:0010192, GO:0008152, GO:004835...      IMP   False   \n",
       "165863  {GO:0065007, BFO:0000015, GO:1900055, GO:00485...      IMP   False   \n",
       "165869  {GO:0003824, GO:0016740, BFO:0000015, GO:00083...      IDA   False   \n",
       "210076  {GO:0003824, GO:0016740, BFO:0000015, GO:00083...      IBA    True   \n",
       "217996  {CARO:0030000, GO:0005794, CARO:0000000, BFO:0...      IBA    True   \n",
       "\n",
       "       negated           pmid                                         pubs  \\\n",
       "56871     None           None           [TAIR:AnalysisReference:501780126]   \n",
       "56872     None           None           [TAIR:AnalysisReference:501780126]   \n",
       "61144     None           None           [TAIR:AnalysisReference:501757242]   \n",
       "85487     None           None           [TAIR:AnalysisReference:501756966]   \n",
       "165846    None  PMID:26690932  [TAIR:Publication:501767599, PMID:26690932]   \n",
       "165851    None  PMID:26690932  [TAIR:Publication:501767599, PMID:26690932]   \n",
       "165856    None  PMID:26690932  [TAIR:Publication:501767599, PMID:26690932]   \n",
       "165858    None  PMID:26690932  [TAIR:Publication:501767599, PMID:26690932]   \n",
       "165863    None  PMID:26690932  [TAIR:Publication:501767599, PMID:26690932]   \n",
       "165869    None  PMID:26690932  [TAIR:Publication:501767599, PMID:26690932]   \n",
       "210076    None           None                             [GO_REF:0000033]   \n",
       "217996    None           None                             [GO_REF:0000033]   \n",
       "\n",
       "           release  \n",
       "56871   2024-11-03  \n",
       "56872   2024-11-03  \n",
       "61144   2024-11-03  \n",
       "85487   2024-11-03  \n",
       "165846  2024-11-03  \n",
       "165851  2024-11-03  \n",
       "165856  2024-11-03  \n",
       "165858  2024-11-03  \n",
       "165863  2024-11-03  \n",
       "165869  2024-11-03  \n",
       "210076  2024-11-03  \n",
       "217996  2024-11-03  "
      ],
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>subject</th>\n",
       "      <th>subject_label</th>\n",
       "      <th>predicate</th>\n",
       "      <th>object</th>\n",
       "      <th>object_label</th>\n",
       "      <th>object_obsoletes</th>\n",
       "      <th>object_uninformative</th>\n",
       "      <th>object_closure</th>\n",
       "      <th>object_closure_redundant</th>\n",
       "      <th>evidence</th>\n",
       "      <th>is_iba</th>\n",
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       "      <th>pmid</th>\n",
       "      <th>pubs</th>\n",
       "      <th>release</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>56871</th>\n",
       "      <td>AGI_LocusCode:AT5G62620</td>\n",
       "      <td>GALT6</td>\n",
       "      <td>located_in</td>\n",
       "      <td>GO:0005794</td>\n",
       "      <td>Golgi apparatus</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0110165, GO:0043231, BFO:0000002, GO:00057...</td>\n",
       "      <td>{CARO:0030000, CARO:0000000, BFO:0000004, GO:0...</td>\n",
       "      <td>ISM</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[TAIR:AnalysisReference:501780126]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56872</th>\n",
       "      <td>AGI_LocusCode:AT5G62620</td>\n",
       "      <td>GALT6</td>\n",
       "      <td>located_in</td>\n",
       "      <td>GO:0005794</td>\n",
       "      <td>Golgi apparatus</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0110165, GO:0043231, BFO:0000002, GO:00057...</td>\n",
       "      <td>{CARO:0030000, CARO:0000000, BFO:0000004, GO:0...</td>\n",
       "      <td>ISM</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[TAIR:AnalysisReference:501780126]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>61144</th>\n",
       "      <td>AGI_LocusCode:AT5G62620</td>\n",
       "      <td>GALT6</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0006486</td>\n",
       "      <td>protein glycosylation</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0008152, BFO:0000015, GO:0009100, GO:00434...</td>\n",
       "      <td>{GO:0009059, GO:0043170, GO:0070085, GO:000815...</td>\n",
       "      <td>IEA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[TAIR:AnalysisReference:501757242]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>85487</th>\n",
       "      <td>AGI_LocusCode:AT5G62620</td>\n",
       "      <td>GALT6</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:0030246</td>\n",
       "      <td>carbohydrate binding</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>{BFO:0000015, GO:0003674, GO:0005488, BFO:0000...</td>\n",
       "      <td>{GO:0003674, BFO:0000015, GO:0005488, BFO:0000...</td>\n",
       "      <td>IEA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[TAIR:AnalysisReference:501756966]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>165846</th>\n",
       "      <td>AGI_LocusCode:AT5G62620</td>\n",
       "      <td>GALT6</td>\n",
       "      <td>located_in</td>\n",
       "      <td>GO:0005794</td>\n",
       "      <td>Golgi apparatus</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0110165, GO:0043231, BFO:0000002, GO:00057...</td>\n",
       "      <td>{CARO:0030000, CARO:0000000, BFO:0000004, GO:0...</td>\n",
       "      <td>IDA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:26690932</td>\n",
       "      <td>[TAIR:Publication:501767599, PMID:26690932]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>165851</th>\n",
       "      <td>AGI_LocusCode:AT5G62620</td>\n",
       "      <td>GALT6</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0010405</td>\n",
       "      <td>arabinogalactan protein metabolic process</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0043170, GO:0044036, GO:0010384, GO:007155...</td>\n",
       "      <td>{GO:0043170, GO:0044036, GO:0071554, GO:000815...</td>\n",
       "      <td>IMP</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:26690932</td>\n",
       "      <td>[TAIR:Publication:501767599, PMID:26690932]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>165856</th>\n",
       "      <td>AGI_LocusCode:AT5G62620</td>\n",
       "      <td>GALT6</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0018258</td>\n",
       "      <td>protein O-linked glycosylation via hydroxyproline</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0006493, GO:0008152, BFO:0000015, GO:00091...</td>\n",
       "      <td>{GO:0009059, GO:0006493, GO:0043170, GO:007008...</td>\n",
       "      <td>IDA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:26690932</td>\n",
       "      <td>[TAIR:Publication:501767599, PMID:26690932]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>165858</th>\n",
       "      <td>AGI_LocusCode:AT5G62620</td>\n",
       "      <td>GALT6</td>\n",
       "      <td>acts_upstream_of_or_within</td>\n",
       "      <td>GO:0048354</td>\n",
       "      <td>mucilage biosynthetic process involved in seed...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0032501, GO:0008152, GO:0048359, BFO:00000...</td>\n",
       "      <td>{GO:0032501, GO:0010192, GO:0008152, GO:004835...</td>\n",
       "      <td>IMP</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:26690932</td>\n",
       "      <td>[TAIR:Publication:501767599, PMID:26690932]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>165863</th>\n",
       "      <td>AGI_LocusCode:AT5G62620</td>\n",
       "      <td>GALT6</td>\n",
       "      <td>acts_upstream_of_or_within</td>\n",
       "      <td>GO:1900056</td>\n",
       "      <td>negative regulation of leaf senescence</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0065007, BFO:0000015, GO:1900055, GO:00485...</td>\n",
       "      <td>{GO:0065007, BFO:0000015, GO:1900055, GO:00485...</td>\n",
       "      <td>IMP</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:26690932</td>\n",
       "      <td>[TAIR:Publication:501767599, PMID:26690932]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>165869</th>\n",
       "      <td>AGI_LocusCode:AT5G62620</td>\n",
       "      <td>GALT6</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:1990714</td>\n",
       "      <td>hydroxyproline O-galactosyltransferase activity</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0003824, GO:0016740, BFO:0000015, GO:00083...</td>\n",
       "      <td>{GO:0003824, GO:0016740, BFO:0000015, GO:00083...</td>\n",
       "      <td>IDA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:26690932</td>\n",
       "      <td>[TAIR:Publication:501767599, PMID:26690932]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>210076</th>\n",
       "      <td>AGI_LocusCode:AT5G62620</td>\n",
       "      <td>GALT6</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:1990714</td>\n",
       "      <td>hydroxyproline O-galactosyltransferase activity</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0003824, GO:0016740, BFO:0000015, GO:00083...</td>\n",
       "      <td>{GO:0003824, GO:0016740, BFO:0000015, GO:00083...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>True</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>217996</th>\n",
       "      <td>AGI_LocusCode:AT5G62620</td>\n",
       "      <td>GALT6</td>\n",
       "      <td>is_active_in</td>\n",
       "      <td>GO:0000139</td>\n",
       "      <td>Golgi membrane</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0110165, GO:0043231, BFO:0000002, GO:00057...</td>\n",
       "      <td>{CARO:0030000, GO:0005794, CARO:0000000, BFO:0...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>True</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ]
     },
     "execution_count": 296,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "execution_count": 296
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:30:51.132969Z",
     "start_time": "2025-01-06T01:30:51.128031Z"
    }
   },
   "cell_type": "code",
   "source": [
    "\n",
    "def create_gene_df(df: pd.DataFrame):\n",
    "    \"\"\"\n",
    "    creates a new dataframe, grouped by gene (subject)\n",
    "    \n",
    "    :param df: \n",
    "    :return: \n",
    "    \"\"\"\n",
    "    gene_df = df.groupby(\"subject\").agg({\n",
    "        \"object\": \"count\",\n",
    "        \"is_iba\": \"sum\",\n",
    "        \"negated\": \"sum\",\n",
    "        # for object, take the union of all distinct values\n",
    "        \"object\": lambda x: set(x),\n",
    "        # for object closure, take the union of all sets\n",
    "        \"object_closure\": lambda x: set.union(*x),\n",
    "        \"object_closure_redundant\": lambda x: set.union(*x),\n",
    "        \"pmid\": lambda x: set(x),\n",
    "        #\"pubs\": lambda x: set.union(set(x)),\n",
    "        \"release\": \"first\",\n",
    "    }).reset_index()\n",
    "    # the redundant closure is the set difference of object_closure and object\n",
    "    gene_df = gene_df.rename(columns={\n",
    "        \"object\": \"terms\",\n",
    "        \"is_iba\": \"n_iba\",\n",
    "        \"negated\": \"n_negated\",\n",
    "        \"object_closure\": \"closure\",\n",
    "        \"pmid\": \"n_pmid\",\n",
    "    })\n",
    "    return gene_df"
   ],
   "id": "41a8190a165c5998",
   "outputs": [],
   "execution_count": 297
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:30:51.940805Z",
     "start_time": "2025-01-06T01:30:51.183316Z"
    }
   },
   "cell_type": "code",
   "source": [
    "gene_df = create_gene_df(df)\n",
    "gene_df"
   ],
   "id": "d44b299cbd15b29e",
   "outputs": [
    {
     "data": {
      "text/plain": [
       "             subject                                              terms  \\\n",
       "0     SGD:S000000001  {GO:0071168, GO:0005739, GO:0008301, GO:000367...   \n",
       "1     SGD:S000000002  {GO:0015031, GO:0099023, GO:0005768, GO:000662...   \n",
       "2     SGD:S000000003  {GO:0005085, GO:0005737, GO:0032232, GO:000582...   \n",
       "3     SGD:S000000004  {GO:0005829, GO:0072671, GO:0005576, GO:003460...   \n",
       "4     SGD:S000000005  {GO:0015031, GO:0006621, GO:0005789, GO:000688...   \n",
       "...              ...                                                ...   \n",
       "6906  SGD:S000350095               {GO:0008150, GO:0003674, GO:0005575}   \n",
       "6907  SGD:S000350096               {GO:0008150, GO:0003674, GO:0005575}   \n",
       "6908  SGD:S000350097               {GO:0005575, GO:0003674, GO:0008150}   \n",
       "6909  SGD:S000350098               {GO:0005575, GO:0003674, GO:0008150}   \n",
       "6910  SGD:S000350099               {GO:0003674, GO:0005575, GO:0008150}   \n",
       "\n",
       "      n_iba n_negated                                            closure  \\\n",
       "0         3         0  {GO:0005739, GO:0000182, GO:0008152, BFO:00000...   \n",
       "1         4         0  {GO:0032509, GO:0071985, GO:0046872, BFO:00000...   \n",
       "2         3         0  {GO:0005085, GO:0030234, GO:0008152, BFO:00000...   \n",
       "3         9         0  {GO:1901363, GO:0003723, GO:0008152, BFO:00000...   \n",
       "4         8         0  {BFO:0000015, GO:0030135, GO:0070972, GO:01101...   \n",
       "...     ...       ...                                                ...   \n",
       "6906      0         0  {BFO:0000003, BFO:0000015, BFO:0000004, GO:000...   \n",
       "6907      0         0  {BFO:0000003, BFO:0000015, BFO:0000004, GO:000...   \n",
       "6908      0         0  {BFO:0000004, BFO:0000002, GO:0003674, GO:0008...   \n",
       "6909      0         0  {BFO:0000004, BFO:0000002, GO:0003674, GO:0008...   \n",
       "6910      0         0  {BFO:0000040, BFO:0000015, BFO:0000004, GO:000...   \n",
       "\n",
       "                               object_closure_redundant  \\\n",
       "0     {GO:0000182, GO:0008152, BFO:0000015, GO:00010...   \n",
       "1     {GO:0032509, GO:0071985, GO:0046872, BFO:00000...   \n",
       "2     {GO:0030234, GO:0008152, BFO:0000015, GO:00900...   \n",
       "3     {GO:1901363, GO:0003723, GO:0008152, BFO:00000...   \n",
       "4     {BFO:0000015, GO:0030135, GO:0070972, GO:01101...   \n",
       "...                                                 ...   \n",
       "6906  {BFO:0000004, BFO:0000040, BFO:0000003, BFO:00...   \n",
       "6907  {BFO:0000004, BFO:0000040, BFO:0000003, BFO:00...   \n",
       "6908  {BFO:0000004, BFO:0000002, BFO:0000003, BFO:00...   \n",
       "6909  {BFO:0000004, BFO:0000002, BFO:0000003, BFO:00...   \n",
       "6910  {BFO:0000004, BFO:0000002, BFO:0000003, BFO:00...   \n",
       "\n",
       "                                                 n_pmid     release  \n",
       "0     {PMID:2404611, PMID:18708580, PMID:2649882, PM...  2024-11-03  \n",
       "1     {PMID:19828734, PMID:30358795, PMID:20173035, ...  2024-11-03  \n",
       "2     {PMID:19545407, PMID:10409717, PMID:17925388, ...  2024-11-03  \n",
       "3     {PMID:18706386, PMID:9789005, PMID:26928762, P...  2024-11-03  \n",
       "4     {PMID:26928762, PMID:10359606, None, PMID:1115...  2024-11-03  \n",
       "...                                                 ...         ...  \n",
       "6906                                             {None}  2024-11-03  \n",
       "6907                                             {None}  2024-11-03  \n",
       "6908                                             {None}  2024-11-03  \n",
       "6909                                             {None}  2024-11-03  \n",
       "6910                                             {None}  2024-11-03  \n",
       "\n",
       "[6911 rows x 8 columns]"
      ],
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>subject</th>\n",
       "      <th>terms</th>\n",
       "      <th>n_iba</th>\n",
       "      <th>n_negated</th>\n",
       "      <th>closure</th>\n",
       "      <th>object_closure_redundant</th>\n",
       "      <th>n_pmid</th>\n",
       "      <th>release</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>SGD:S000000001</td>\n",
       "      <td>{GO:0071168, GO:0005739, GO:0008301, GO:000367...</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>{GO:0005739, GO:0000182, GO:0008152, BFO:00000...</td>\n",
       "      <td>{GO:0000182, GO:0008152, BFO:0000015, GO:00010...</td>\n",
       "      <td>{PMID:2404611, PMID:18708580, PMID:2649882, PM...</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>SGD:S000000002</td>\n",
       "      <td>{GO:0015031, GO:0099023, GO:0005768, GO:000662...</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>{GO:0032509, GO:0071985, GO:0046872, BFO:00000...</td>\n",
       "      <td>{GO:0032509, GO:0071985, GO:0046872, BFO:00000...</td>\n",
       "      <td>{PMID:19828734, PMID:30358795, PMID:20173035, ...</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>SGD:S000000003</td>\n",
       "      <td>{GO:0005085, GO:0005737, GO:0032232, GO:000582...</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>{GO:0005085, GO:0030234, GO:0008152, BFO:00000...</td>\n",
       "      <td>{GO:0030234, GO:0008152, BFO:0000015, GO:00900...</td>\n",
       "      <td>{PMID:19545407, PMID:10409717, PMID:17925388, ...</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>SGD:S000000004</td>\n",
       "      <td>{GO:0005829, GO:0072671, GO:0005576, GO:003460...</td>\n",
       "      <td>9</td>\n",
       "      <td>0</td>\n",
       "      <td>{GO:1901363, GO:0003723, GO:0008152, BFO:00000...</td>\n",
       "      <td>{GO:1901363, GO:0003723, GO:0008152, BFO:00000...</td>\n",
       "      <td>{PMID:18706386, PMID:9789005, PMID:26928762, P...</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>SGD:S000000005</td>\n",
       "      <td>{GO:0015031, GO:0006621, GO:0005789, GO:000688...</td>\n",
       "      <td>8</td>\n",
       "      <td>0</td>\n",
       "      <td>{BFO:0000015, GO:0030135, GO:0070972, GO:01101...</td>\n",
       "      <td>{BFO:0000015, GO:0030135, GO:0070972, GO:01101...</td>\n",
       "      <td>{PMID:26928762, PMID:10359606, None, PMID:1115...</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6906</th>\n",
       "      <td>SGD:S000350095</td>\n",
       "      <td>{GO:0008150, GO:0003674, GO:0005575}</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>{BFO:0000003, BFO:0000015, BFO:0000004, GO:000...</td>\n",
       "      <td>{BFO:0000004, BFO:0000040, BFO:0000003, BFO:00...</td>\n",
       "      <td>{None}</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6907</th>\n",
       "      <td>SGD:S000350096</td>\n",
       "      <td>{GO:0008150, GO:0003674, GO:0005575}</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>{BFO:0000003, BFO:0000015, BFO:0000004, GO:000...</td>\n",
       "      <td>{BFO:0000004, BFO:0000040, BFO:0000003, BFO:00...</td>\n",
       "      <td>{None}</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6908</th>\n",
       "      <td>SGD:S000350097</td>\n",
       "      <td>{GO:0005575, GO:0003674, GO:0008150}</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>{BFO:0000004, BFO:0000002, GO:0003674, GO:0008...</td>\n",
       "      <td>{BFO:0000004, BFO:0000002, BFO:0000003, BFO:00...</td>\n",
       "      <td>{None}</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6909</th>\n",
       "      <td>SGD:S000350098</td>\n",
       "      <td>{GO:0005575, GO:0003674, GO:0008150}</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>{BFO:0000004, BFO:0000002, GO:0003674, GO:0008...</td>\n",
       "      <td>{BFO:0000004, BFO:0000002, BFO:0000003, BFO:00...</td>\n",
       "      <td>{None}</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6910</th>\n",
       "      <td>SGD:S000350099</td>\n",
       "      <td>{GO:0003674, GO:0005575, GO:0008150}</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>{BFO:0000040, BFO:0000015, BFO:0000004, GO:000...</td>\n",
       "      <td>{BFO:0000004, BFO:0000002, BFO:0000003, BFO:00...</td>\n",
       "      <td>{None}</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>6911 rows × 8 columns</p>\n",
       "</div>"
      ]
     },
     "execution_count": 298,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "execution_count": 298
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:30:51.980756Z",
     "start_time": "2025-01-06T01:30:51.976257Z"
    }
   },
   "cell_type": "code",
   "source": [
    "def set_redundant_flag(assocs: pd.DataFrame, gene_df: pd.DataFrame):\n",
    "    \"\"\"\n",
    "    Sets the redundant flag for each association, if the object is in object_closure_redundant for that gene.\n",
    "    \n",
    "    :param assocs: \n",
    "    :param gene_df: \n",
    "    :return: \n",
    "    \"\"\"\n",
    "    # Create a mapping of subject to object_closure_redundant\n",
    "    redundant_map = gene_df.set_index('subject')['object_closure_redundant'].to_dict()\n",
    "    \n",
    "    # Vectorized check for each row\n",
    "    def check_redundant(row):\n",
    "        if row['is_iba']:\n",
    "            return False\n",
    "        closure_set = redundant_map.get(row['subject'], set())\n",
    "        is_redundant = row['object'] in closure_set\n",
    "        return is_redundant\n",
    "    \n",
    "    # Apply the check to all rows at once\n",
    "    assocs['redundant'] = assocs.apply(check_redundant, axis=1)"
   ],
   "id": "14019377b3f59d2d",
   "outputs": [],
   "execution_count": 299
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:30:52.035318Z",
     "start_time": "2025-01-06T01:30:52.032340Z"
    }
   },
   "cell_type": "code",
   "source": "df[\"redundant\"] = False",
   "id": "e288d1b3e5994388",
   "outputs": [],
   "execution_count": 300
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:30:53.104422Z",
     "start_time": "2025-01-06T01:30:52.043397Z"
    }
   },
   "cell_type": "code",
   "source": "set_redundant_flag(df, gene_df)",
   "id": "3600b3b1a3c349c3",
   "outputs": [],
   "execution_count": 301
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:31:06.845590Z",
     "start_time": "2025-01-06T01:31:06.820270Z"
    }
   },
   "cell_type": "code",
   "source": "df[df['redundant']]",
   "id": "aa7fd8e88c4dbf6",
   "outputs": [
    {
     "data": {
      "text/plain": [
       "               subject subject_label                   predicate      object  \\\n",
       "16      SGD:S000004539          FPR3                  located_in  GO:0005634   \n",
       "28      SGD:S000002699          HRQ1                     enables  GO:0043138   \n",
       "33      SGD:S000002699          HRQ1                     enables  GO:0043138   \n",
       "39      SGD:S000003245         SNU71                  located_in  GO:0005634   \n",
       "42      SGD:S000001443          DJP1  acts_upstream_of_or_within  GO:0006626   \n",
       "...                ...           ...                         ...         ...   \n",
       "105624  SGD:S000006483       RDN18-2                  located_in  GO:0005840   \n",
       "105625  SGD:S000006502         SNR42                  located_in  GO:0005730   \n",
       "105627  SGD:S000007300         SNR36                  located_in  GO:0005730   \n",
       "105628  SGD:S000006484       RDN25-1                  located_in  GO:0005840   \n",
       "105629  SGD:S000006485       RDN25-2                  located_in  GO:0005840   \n",
       "\n",
       "                              object_label  object_obsoletes  \\\n",
       "16                                 nucleus             False   \n",
       "28             3'-5' DNA helicase activity             False   \n",
       "33             3'-5' DNA helicase activity             False   \n",
       "39                                 nucleus             False   \n",
       "42      protein targeting to mitochondrion             False   \n",
       "...                                    ...               ...   \n",
       "105624                            ribosome             False   \n",
       "105625                           nucleolus             False   \n",
       "105627                           nucleolus             False   \n",
       "105628                            ribosome             False   \n",
       "105629                            ribosome             False   \n",
       "\n",
       "        object_uninformative  \\\n",
       "16                     False   \n",
       "28                     False   \n",
       "33                     False   \n",
       "39                     False   \n",
       "42                     False   \n",
       "...                      ...   \n",
       "105624                 False   \n",
       "105625                 False   \n",
       "105627                 False   \n",
       "105628                 False   \n",
       "105629                 False   \n",
       "\n",
       "                                           object_closure  \\\n",
       "16      {GO:0110165, GO:0043231, BFO:0000002, GO:00432...   \n",
       "28      {BFO:0000015, GO:0008150, GO:0016043, GO:00431...   \n",
       "33      {BFO:0000015, GO:0008150, GO:0016043, GO:00431...   \n",
       "39      {GO:0110165, GO:0043231, BFO:0000002, GO:00432...   \n",
       "42      {GO:0070585, GO:0051234, GO:0006605, GO:007072...   \n",
       "...                                                   ...   \n",
       "105624  {GO:0110165, BFO:0000002, GO:0043229, CL:00000...   \n",
       "105625  {GO:0043233, GO:0043231, GO:0110165, BFO:00000...   \n",
       "105627  {GO:0043233, GO:0043231, GO:0110165, BFO:00000...   \n",
       "105628  {GO:0110165, BFO:0000002, GO:0043229, CL:00000...   \n",
       "105629  {GO:0110165, BFO:0000002, GO:0043229, CL:00000...   \n",
       "\n",
       "                                 object_closure_redundant evidence  is_iba  \\\n",
       "16      {CARO:0030000, CARO:0000000, BFO:0000004, GO:0...      IDA   False   \n",
       "28      {GO:0140097, GO:0032508, GO:0003824, BFO:00000...      IDA   False   \n",
       "33      {GO:0140097, GO:0032508, GO:0003824, BFO:00000...      IDA   False   \n",
       "39      {CARO:0030000, CARO:0000000, BFO:0000004, GO:0...      IEA   False   \n",
       "42      {GO:0070585, GO:0070727, GO:0033365, BFO:00000...      IMP   False   \n",
       "...                                                   ...      ...     ...   \n",
       "105624  {CARO:0030000, CARO:0000000, BFO:0000004, GO:0...      IEA   False   \n",
       "105625  {CARO:0030000, GO:0005634, CARO:0000000, BFO:0...      IEA   False   \n",
       "105627  {CARO:0030000, GO:0005634, CARO:0000000, BFO:0...      IEA   False   \n",
       "105628  {CARO:0030000, CARO:0000000, BFO:0000004, GO:0...      IEA   False   \n",
       "105629  {CARO:0030000, CARO:0000000, BFO:0000004, GO:0...      IEA   False   \n",
       "\n",
       "       negated           pmid              pubs     release  redundant  \n",
       "16        None  PMID:26359986   [PMID:26359986]  2024-11-03       True  \n",
       "28        None  PMID:28385527   [PMID:28385527]  2024-11-03       True  \n",
       "33        None  PMID:24440721   [PMID:24440721]  2024-11-03       True  \n",
       "39        None           None  [GO_REF:0000043]  2024-11-03       True  \n",
       "42        None  PMID:30213914   [PMID:30213914]  2024-11-03       True  \n",
       "...        ...            ...               ...         ...        ...  \n",
       "105624    None  PMID:30502926   [PMID:30502926]  2024-11-03       True  \n",
       "105625    None  PMID:30502926   [PMID:30502926]  2024-11-03       True  \n",
       "105627    None  PMID:30502926   [PMID:30502926]  2024-11-03       True  \n",
       "105628    None  PMID:30502926   [PMID:30502926]  2024-11-03       True  \n",
       "105629    None  PMID:30502926   [PMID:30502926]  2024-11-03       True  \n",
       "\n",
       "[34441 rows x 16 columns]"
      ],
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>subject</th>\n",
       "      <th>subject_label</th>\n",
       "      <th>predicate</th>\n",
       "      <th>object</th>\n",
       "      <th>object_label</th>\n",
       "      <th>object_obsoletes</th>\n",
       "      <th>object_uninformative</th>\n",
       "      <th>object_closure</th>\n",
       "      <th>object_closure_redundant</th>\n",
       "      <th>evidence</th>\n",
       "      <th>is_iba</th>\n",
       "      <th>negated</th>\n",
       "      <th>pmid</th>\n",
       "      <th>pubs</th>\n",
       "      <th>release</th>\n",
       "      <th>redundant</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>SGD:S000004539</td>\n",
       "      <td>FPR3</td>\n",
       "      <td>located_in</td>\n",
       "      <td>GO:0005634</td>\n",
       "      <td>nucleus</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0110165, GO:0043231, BFO:0000002, GO:00432...</td>\n",
       "      <td>{CARO:0030000, CARO:0000000, BFO:0000004, GO:0...</td>\n",
       "      <td>IDA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:26359986</td>\n",
       "      <td>[PMID:26359986]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>SGD:S000002699</td>\n",
       "      <td>HRQ1</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:0043138</td>\n",
       "      <td>3'-5' DNA helicase activity</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{BFO:0000015, GO:0008150, GO:0016043, GO:00431...</td>\n",
       "      <td>{GO:0140097, GO:0032508, GO:0003824, BFO:00000...</td>\n",
       "      <td>IDA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:28385527</td>\n",
       "      <td>[PMID:28385527]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>33</th>\n",
       "      <td>SGD:S000002699</td>\n",
       "      <td>HRQ1</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:0043138</td>\n",
       "      <td>3'-5' DNA helicase activity</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{BFO:0000015, GO:0008150, GO:0016043, GO:00431...</td>\n",
       "      <td>{GO:0140097, GO:0032508, GO:0003824, BFO:00000...</td>\n",
       "      <td>IDA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:24440721</td>\n",
       "      <td>[PMID:24440721]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>39</th>\n",
       "      <td>SGD:S000003245</td>\n",
       "      <td>SNU71</td>\n",
       "      <td>located_in</td>\n",
       "      <td>GO:0005634</td>\n",
       "      <td>nucleus</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0110165, GO:0043231, BFO:0000002, GO:00432...</td>\n",
       "      <td>{CARO:0030000, CARO:0000000, BFO:0000004, GO:0...</td>\n",
       "      <td>IEA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[GO_REF:0000043]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42</th>\n",
       "      <td>SGD:S000001443</td>\n",
       "      <td>DJP1</td>\n",
       "      <td>acts_upstream_of_or_within</td>\n",
       "      <td>GO:0006626</td>\n",
       "      <td>protein targeting to mitochondrion</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0070585, GO:0051234, GO:0006605, GO:007072...</td>\n",
       "      <td>{GO:0070585, GO:0070727, GO:0033365, BFO:00000...</td>\n",
       "      <td>IMP</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:30213914</td>\n",
       "      <td>[PMID:30213914]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>105624</th>\n",
       "      <td>SGD:S000006483</td>\n",
       "      <td>RDN18-2</td>\n",
       "      <td>located_in</td>\n",
       "      <td>GO:0005840</td>\n",
       "      <td>ribosome</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0110165, BFO:0000002, GO:0043229, CL:00000...</td>\n",
       "      <td>{CARO:0030000, CARO:0000000, BFO:0000004, GO:0...</td>\n",
       "      <td>IEA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:30502926</td>\n",
       "      <td>[PMID:30502926]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>105625</th>\n",
       "      <td>SGD:S000006502</td>\n",
       "      <td>SNR42</td>\n",
       "      <td>located_in</td>\n",
       "      <td>GO:0005730</td>\n",
       "      <td>nucleolus</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0043233, GO:0043231, GO:0110165, BFO:00000...</td>\n",
       "      <td>{CARO:0030000, GO:0005634, CARO:0000000, BFO:0...</td>\n",
       "      <td>IEA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:30502926</td>\n",
       "      <td>[PMID:30502926]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>105627</th>\n",
       "      <td>SGD:S000007300</td>\n",
       "      <td>SNR36</td>\n",
       "      <td>located_in</td>\n",
       "      <td>GO:0005730</td>\n",
       "      <td>nucleolus</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0043233, GO:0043231, GO:0110165, BFO:00000...</td>\n",
       "      <td>{CARO:0030000, GO:0005634, CARO:0000000, BFO:0...</td>\n",
       "      <td>IEA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:30502926</td>\n",
       "      <td>[PMID:30502926]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>105628</th>\n",
       "      <td>SGD:S000006484</td>\n",
       "      <td>RDN25-1</td>\n",
       "      <td>located_in</td>\n",
       "      <td>GO:0005840</td>\n",
       "      <td>ribosome</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0110165, BFO:0000002, GO:0043229, CL:00000...</td>\n",
       "      <td>{CARO:0030000, CARO:0000000, BFO:0000004, GO:0...</td>\n",
       "      <td>IEA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:30502926</td>\n",
       "      <td>[PMID:30502926]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>105629</th>\n",
       "      <td>SGD:S000006485</td>\n",
       "      <td>RDN25-2</td>\n",
       "      <td>located_in</td>\n",
       "      <td>GO:0005840</td>\n",
       "      <td>ribosome</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0110165, BFO:0000002, GO:0043229, CL:00000...</td>\n",
       "      <td>{CARO:0030000, CARO:0000000, BFO:0000004, GO:0...</td>\n",
       "      <td>IEA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:30502926</td>\n",
       "      <td>[PMID:30502926]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>34441 rows × 16 columns</p>\n",
       "</div>"
      ]
     },
     "execution_count": 302,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "execution_count": 302
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:31:20.496519Z",
     "start_time": "2025-01-06T01:31:20.492087Z"
    }
   },
   "cell_type": "code",
   "source": [
    "def annotate_new_pubs(assocs: pd.DataFrame, prev_assocs: pd.DataFrame):\n",
    "    \"\"\"\n",
    "    Annotates each association in assocs with fresh if its pmid is not in prev_assocs.\n",
    "    \n",
    "    :param assocs\n",
    "    \"\"\"\n",
    "    prev_pmid_map = prev_assocs.set_index('pmid')['subject'].to_dict()\n",
    "    \n",
    "    # Vectorized check for each row\n",
    "    def check_new(row):\n",
    "        return row['pmid'] not in prev_pmid_map\n",
    "    \n",
    "    # Apply the check to all rows in prev_assocs\n",
    "    assocs['pmid_new'] = assocs.apply(check_new, axis=1)\n",
    "    \n",
    "    # annotate tuple as unique if (subject, object) is not in prev\n",
    "    prev_pair_assocs = set(zip(prev_assocs['subject'], prev_assocs['object']))\n",
    "    assocs['is_new'] = ~assocs.apply(lambda x: (x['subject'], x['object']) in prev_pair_assocs, axis=1)\n",
    "    \n",
    "    assocs['fresh'] = assocs['pmid_new'] & assocs['is_new']\n",
    "    \n",
    "    "
   ],
   "id": "f2b050545c0fc3a2",
   "outputs": [],
   "execution_count": 303
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:31:20.550163Z",
     "start_time": "2025-01-06T01:31:20.545824Z"
    }
   },
   "cell_type": "code",
   "source": [
    "def annotate_redacted_pubs(assocs: pd.DataFrame, prev_assocs: pd.DataFrame):\n",
    "    \"\"\"\n",
    "    Annotates each association in prev_assocs with retracted if its pmid is not in assocs (latest).\n",
    "    \n",
    "    :param assocs\n",
    "    \"\"\"\n",
    "    # Create a mapping of pmid to subject\n",
    "    pmid_map = assocs.set_index('pmid')['subject'].to_dict()\n",
    "    \n",
    "    # Vectorized check for each row\n",
    "    def check_removed(row):\n",
    "        return row['pmid'] not in pmid_map\n",
    "    \n",
    "    # Apply the check to all rows in prev_assocs\n",
    "    prev_assocs['pmid_removed'] = prev_assocs.apply(check_removed, axis=1)\n",
    "    \n",
    "    # annotate tuple as unique if (subject, object) is not in latest\n",
    "    pair_assocs = set(zip(assocs['subject'], assocs['object']))\n",
    "    prev_assocs['unique'] = ~prev_assocs.apply(lambda x: (x['subject'], x['object']) in pair_assocs, axis=1)\n",
    "    \n",
    "    prev_assocs['redacted'] = prev_assocs['pmid_removed'] & prev_assocs['unique']\n",
    "    \n",
    "    "
   ],
   "id": "867b7a7698c36e29",
   "outputs": [],
   "execution_count": 304
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:31:22.218998Z",
     "start_time": "2025-01-06T01:31:20.571207Z"
    }
   },
   "cell_type": "code",
   "source": "annotate_redacted_pubs(df, prev_df)\n",
   "id": "1b9be34d02fcc35a",
   "outputs": [],
   "execution_count": 305
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:31:35.780825Z",
     "start_time": "2025-01-06T01:31:35.778359Z"
    }
   },
   "cell_type": "code",
   "source": "#prev_df['redacted'] = prev_df['pmid_removed'] & prev_df['unique']",
   "id": "aa4f921bd715ed2e",
   "outputs": [],
   "execution_count": 306
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:31:49.384082Z",
     "start_time": "2025-01-06T01:31:49.381860Z"
    }
   },
   "cell_type": "code",
   "source": "",
   "id": "278a7973e3ec4b32",
   "outputs": [],
   "execution_count": null
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:32:03.236009Z",
     "start_time": "2025-01-06T01:32:03.233785Z"
    }
   },
   "cell_type": "code",
   "source": "#list(set(df['subject']))[:5]",
   "id": "cf5c19ae2c553e2f",
   "outputs": [],
   "execution_count": 307
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:32:16.839927Z",
     "start_time": "2025-01-06T01:32:16.837676Z"
    }
   },
   "cell_type": "code",
   "source": [
    "#iba_df = df[df['is_iba']]\n",
    "#iba_subjects = set(iba_df['subject'])\n",
    "#list(iba_subjects)[:5]"
   ],
   "id": "62ece9e9f658c81c",
   "outputs": [],
   "execution_count": 308
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:32:30.496156Z",
     "start_time": "2025-01-06T01:32:30.491391Z"
    }
   },
   "cell_type": "code",
   "source": [
    "def set_iba_status(assocs: pd.DataFrame):\n",
    "    iba_df = assocs[assocs['is_iba']]\n",
    "    iba_subjects = set(iba_df['subject'])\n",
    "    # set the IBA rejected as associations for which\n",
    "    # (a) the subject has an IBA association\n",
    "    # (b) the object is not in the closure of the object in the IBA association\n",
    "    # first we set the iba closure for each subject\n",
    "    iba_closure = iba_df.groupby('subject')['object_closure'].aggregate(lambda x: set.union(*x)).to_dict()\n",
    "    # now we set IBA rejected for each row\n",
    "    def check_iba_rejected(row):\n",
    "        if row['is_iba']:\n",
    "            return False\n",
    "        return row['subject'] in iba_subjects and row['object'] not in iba_closure.get(row['subject'], set())\n",
    "        #if row['subject'].startswith(\"TAIR\"):\n",
    "        #    print(f\"Checking {row['subject']} in {list(iba_subjects)[:5]}\")\n",
    "        #return row['subject'] in iba_subjects\n",
    "        #return True\n",
    "    \n",
    "    assocs['iba_rejected'] = assocs.apply(check_iba_rejected, axis=1)\n",
    "\n",
    "#set_iba_status(df)\n",
    "    \n",
    "    "
   ],
   "id": "8f206c911adcb70",
   "outputs": [],
   "execution_count": 309
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:32:44.180038Z",
     "start_time": "2025-01-06T01:32:44.177926Z"
    }
   },
   "cell_type": "code",
   "source": "",
   "id": "a0467e309db76da1",
   "outputs": [],
   "execution_count": null
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:32:57.830022Z",
     "start_time": "2025-01-06T01:32:57.814205Z"
    }
   },
   "cell_type": "code",
   "source": "human_df",
   "id": "1a73a4e32fb7090f",
   "outputs": [
    {
     "data": {
      "text/plain": [
       "                     subject subject_label    predicate      object  \\\n",
       "0       UniProtKB:A0A024RBG1        NUDT4B      enables  GO:0003723   \n",
       "1       UniProtKB:A0A024RBG1        NUDT4B      enables  GO:0005515   \n",
       "2       UniProtKB:A0A024RBG1        NUDT4B      enables  GO:0046872   \n",
       "3       UniProtKB:A0A024RBG1        NUDT4B   located_in  GO:0005829   \n",
       "4       UniProtKB:A0A075B6H5   TRBV20OR9-2  involved_in  GO:0002376   \n",
       "...                      ...           ...          ...         ...   \n",
       "782818      UniProtKB:Q9NZC2         TREM2  involved_in  GO:0045088   \n",
       "782819      UniProtKB:Q9Y2K2          SIK3      enables  GO:0050321   \n",
       "782820      UniProtKB:P43235          CTSK  involved_in  GO:0051603   \n",
       "782821      UniProtKB:Q07343         PDE4B      enables  GO:0047555   \n",
       "782822      UniProtKB:A6NC42         DPPA5  involved_in  GO:0010468   \n",
       "\n",
       "                                             object_label  object_obsoletes  \\\n",
       "0                                             RNA binding             False   \n",
       "1                                         protein binding             False   \n",
       "2                                       metal ion binding             False   \n",
       "3                                                 cytosol             False   \n",
       "4                                   immune system process             False   \n",
       "...                                                   ...               ...   \n",
       "782818               regulation of innate immune response             False   \n",
       "782819                        tau-protein kinase activity             False   \n",
       "782820  proteolysis involved in protein catabolic process             False   \n",
       "782821        3',5'-cyclic-GMP phosphodiesterase activity             False   \n",
       "782822                      regulation of gene expression             False   \n",
       "\n",
       "        object_uninformative  \\\n",
       "0                       True   \n",
       "1                       True   \n",
       "2                       True   \n",
       "3                      False   \n",
       "4                      False   \n",
       "...                      ...   \n",
       "782818                 False   \n",
       "782819                 False   \n",
       "782820                 False   \n",
       "782821                 False   \n",
       "782822                 False   \n",
       "\n",
       "                                           object_closure  \\\n",
       "0       {GO:0097159, GO:0003723, BFO:0000015, GO:00036...   \n",
       "1       {BFO:0000015, GO:0003674, GO:0005488, BFO:0000...   \n",
       "2       {GO:0043169, GO:0046872, BFO:0000015, GO:00360...   \n",
       "3       {CARO:0030000, UBERON:0000061, CARO:0000003, G...   \n",
       "4       {GO:0008150, BFO:0000015, GO:0002376, BFO:0000...   \n",
       "...                                                   ...   \n",
       "782818  {GO:0065007, GO:0002682, GO:0050776, BFO:00000...   \n",
       "782819  {GO:0140096, GO:0003824, GO:0004674, GO:001674...   \n",
       "782820  {GO:0043170, GO:0006508, GO:0044238, GO:000905...   \n",
       "782821  {GO:0047555, GO:0003824, GO:0008081, BFO:00000...   \n",
       "782822  {GO:0065007, GO:0060255, GO:0009889, BFO:00000...   \n",
       "\n",
       "                                 object_closure_redundant evidence  is_iba  \\\n",
       "0       {GO:0097159, BFO:0000015, GO:0003674, GO:00036...      IEA   False   \n",
       "1       {GO:0003674, BFO:0000015, GO:0005488, BFO:0000...      IPI   False   \n",
       "2       {GO:0043169, BFO:0000015, GO:0036094, GO:00431...      IEA   False   \n",
       "3       {CARO:0030000, CARO:0000000, BFO:0000004, GO:0...      IDA   False   \n",
       "4                  {BFO:0000015, GO:0008150, BFO:0000003}      IEA   False   \n",
       "...                                                   ...      ...     ...   \n",
       "782818  {GO:0065007, GO:0002682, GO:0050776, BFO:00000...      IBA    True   \n",
       "782819  {GO:0140096, GO:0003824, GO:0004674, GO:001674...      IBA    True   \n",
       "782820  {GO:0043170, GO:0006508, GO:0044238, GO:000905...      IBA    True   \n",
       "782821  {GO:0003824, GO:0008081, BFO:0000015, GO:00425...      IBA    True   \n",
       "782822  {GO:0065007, GO:0060255, GO:0009889, BFO:00000...      IBA    True   \n",
       "\n",
       "       negated           pmid              pubs     release  \n",
       "0         None           None  [GO_REF:0000043]  2024-11-03  \n",
       "1         None  PMID:33961781   [PMID:33961781]  2024-11-03  \n",
       "2         None           None  [GO_REF:0000043]  2024-11-03  \n",
       "3         None           None  [GO_REF:0000052]  2024-11-03  \n",
       "4         None           None  [GO_REF:0000043]  2024-11-03  \n",
       "...        ...            ...               ...         ...  \n",
       "782818    None           None  [GO_REF:0000033]  2024-11-03  \n",
       "782819    None           None  [GO_REF:0000033]  2024-11-03  \n",
       "782820    None           None  [GO_REF:0000033]  2024-11-03  \n",
       "782821    None           None  [GO_REF:0000033]  2024-11-03  \n",
       "782822    None           None  [GO_REF:0000033]  2024-11-03  \n",
       "\n",
       "[782823 rows x 15 columns]"
      ],
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>subject</th>\n",
       "      <th>subject_label</th>\n",
       "      <th>predicate</th>\n",
       "      <th>object</th>\n",
       "      <th>object_label</th>\n",
       "      <th>object_obsoletes</th>\n",
       "      <th>object_uninformative</th>\n",
       "      <th>object_closure</th>\n",
       "      <th>object_closure_redundant</th>\n",
       "      <th>evidence</th>\n",
       "      <th>is_iba</th>\n",
       "      <th>negated</th>\n",
       "      <th>pmid</th>\n",
       "      <th>pubs</th>\n",
       "      <th>release</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>UniProtKB:A0A024RBG1</td>\n",
       "      <td>NUDT4B</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:0003723</td>\n",
       "      <td>RNA binding</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>{GO:0097159, GO:0003723, BFO:0000015, GO:00036...</td>\n",
       "      <td>{GO:0097159, BFO:0000015, GO:0003674, GO:00036...</td>\n",
       "      <td>IEA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[GO_REF:0000043]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>UniProtKB:A0A024RBG1</td>\n",
       "      <td>NUDT4B</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:0005515</td>\n",
       "      <td>protein binding</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>{BFO:0000015, GO:0003674, GO:0005488, BFO:0000...</td>\n",
       "      <td>{GO:0003674, BFO:0000015, GO:0005488, BFO:0000...</td>\n",
       "      <td>IPI</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:33961781</td>\n",
       "      <td>[PMID:33961781]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>UniProtKB:A0A024RBG1</td>\n",
       "      <td>NUDT4B</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:0046872</td>\n",
       "      <td>metal ion binding</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>{GO:0043169, GO:0046872, BFO:0000015, GO:00360...</td>\n",
       "      <td>{GO:0043169, BFO:0000015, GO:0036094, GO:00431...</td>\n",
       "      <td>IEA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[GO_REF:0000043]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>UniProtKB:A0A024RBG1</td>\n",
       "      <td>NUDT4B</td>\n",
       "      <td>located_in</td>\n",
       "      <td>GO:0005829</td>\n",
       "      <td>cytosol</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{CARO:0030000, UBERON:0000061, CARO:0000003, G...</td>\n",
       "      <td>{CARO:0030000, CARO:0000000, BFO:0000004, GO:0...</td>\n",
       "      <td>IDA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[GO_REF:0000052]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>UniProtKB:A0A075B6H5</td>\n",
       "      <td>TRBV20OR9-2</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0002376</td>\n",
       "      <td>immune system process</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0008150, BFO:0000015, GO:0002376, BFO:0000...</td>\n",
       "      <td>{BFO:0000015, GO:0008150, BFO:0000003}</td>\n",
       "      <td>IEA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[GO_REF:0000043]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>782818</th>\n",
       "      <td>UniProtKB:Q9NZC2</td>\n",
       "      <td>TREM2</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0045088</td>\n",
       "      <td>regulation of innate immune response</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0065007, GO:0002682, GO:0050776, BFO:00000...</td>\n",
       "      <td>{GO:0065007, GO:0002682, GO:0050776, BFO:00000...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>True</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>782819</th>\n",
       "      <td>UniProtKB:Q9Y2K2</td>\n",
       "      <td>SIK3</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:0050321</td>\n",
       "      <td>tau-protein kinase activity</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0140096, GO:0003824, GO:0004674, GO:001674...</td>\n",
       "      <td>{GO:0140096, GO:0003824, GO:0004674, GO:001674...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>True</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>782820</th>\n",
       "      <td>UniProtKB:P43235</td>\n",
       "      <td>CTSK</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0051603</td>\n",
       "      <td>proteolysis involved in protein catabolic process</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0043170, GO:0006508, GO:0044238, GO:000905...</td>\n",
       "      <td>{GO:0043170, GO:0006508, GO:0044238, GO:000905...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>True</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>782821</th>\n",
       "      <td>UniProtKB:Q07343</td>\n",
       "      <td>PDE4B</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:0047555</td>\n",
       "      <td>3',5'-cyclic-GMP phosphodiesterase activity</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0047555, GO:0003824, GO:0008081, BFO:00000...</td>\n",
       "      <td>{GO:0003824, GO:0008081, BFO:0000015, GO:00425...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>True</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>782822</th>\n",
       "      <td>UniProtKB:A6NC42</td>\n",
       "      <td>DPPA5</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0010468</td>\n",
       "      <td>regulation of gene expression</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0065007, GO:0060255, GO:0009889, BFO:00000...</td>\n",
       "      <td>{GO:0065007, GO:0060255, GO:0009889, BFO:00000...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>True</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>782823 rows × 15 columns</p>\n",
       "</div>"
      ]
     },
     "execution_count": 310,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "execution_count": 310
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:33:13.375537Z",
     "start_time": "2025-01-06T01:33:11.321465Z"
    }
   },
   "cell_type": "code",
   "source": "set_iba_status(test_df)",
   "id": "18c85a1e496789a1",
   "outputs": [],
   "execution_count": 311
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:33:15.209395Z",
     "start_time": "2025-01-06T01:33:15.204477Z"
    }
   },
   "cell_type": "code",
   "source": "test_df['iba_rejected'].unique()",
   "id": "f10034b185842dc7",
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([False,  True])"
      ]
     },
     "execution_count": 312,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "execution_count": 312
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:33:28.881918Z",
     "start_time": "2025-01-06T01:33:28.879910Z"
    }
   },
   "cell_type": "code",
   "source": "#set_iba_status(df)",
   "id": "9af1de25e37ec772",
   "outputs": [],
   "execution_count": 313
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:33:42.336419Z",
     "start_time": "2025-01-06T01:33:42.334842Z"
    }
   },
   "cell_type": "code",
   "source": "",
   "id": "906cee0981042c2",
   "outputs": [],
   "execution_count": null
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:33:56.131239Z",
     "start_time": "2025-01-06T01:33:56.126586Z"
    }
   },
   "cell_type": "code",
   "source": [
    "def synthesize(grp: str) -> pd.DataFrame:\n",
    "    \"\"\"\n",
    "    Synthesizes the above steps\n",
    "    \"\"\"\n",
    "    assocs = assocs_to_df(db[grp][LATEST], LATEST)\n",
    "    prev_df_sets = []\n",
    "    for prev in PREVIOUS:\n",
    "        this_prev_assocs = assocs_to_df(db[grp][prev], prev)\n",
    "        prev_df_sets.append(this_prev_assocs)\n",
    "    annotate_new_pubs(assocs, prev_df_sets[0])\n",
    "    #prev_assocs = pd.concat(prev_df_sets).drop_duplicates()\n",
    "    prev_assocs = pd.concat(prev_df_sets)\n",
    "    # prev_assocs = assocs_to_df(db[grp][PREVIOUS[0]], PREVIOUS[0])\n",
    "    repair_assocs_df(assocs)\n",
    "    repair_assocs_df(prev_assocs)\n",
    "    # Create a gene dataframe (for latest only)\n",
    "    gene_df = create_gene_df(assocs)\n",
    "    annotate_redacted_pubs(assocs, prev_assocs)\n",
    "    new_assocs = pd.concat([assocs, prev_assocs[prev_assocs['redacted']]])\n",
    "    set_redundant_flag(new_assocs, gene_df)\n",
    "    set_iba_status(new_assocs)\n",
    "    return new_assocs\n",
    "    \n",
    "    "
   ],
   "id": "a4c3b5106e007c89",
   "outputs": [],
   "execution_count": 314
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:43:49.335421Z",
     "start_time": "2025-01-06T01:34:09.648173Z"
    }
   },
   "cell_type": "code",
   "source": "new_human = synthesize(\"goa_human\")",
   "id": "91b0622de603be32",
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Multiple IDs for 64 labels\n",
      "[('AKAP7', ['UniProtKB:O43687', 'UniProtKB:Q9P0M2']), ('ARHGEF18', ['UniProtKB:A0A590UK10', 'UniProtKB:Q6ZSZ5']), ('BBC3', ['UniProtKB:Q9BXH1', 'UniProtKB:Q96PG8']), ('CALCA', ['UniProtKB:P06881', 'UniProtKB:P01258']), ('CDKN2A', ['UniProtKB:Q8N726', 'UniProtKB:P42771'])]\n",
      "Multiple IDs for 100 labels\n",
      "[('AKAP7', ['UniProtKB:O43687', 'UniProtKB:Q9P0M2']), ('AMY1A', ['UniProtKB:P04745', 'UniProtKB:P0DUB6']), ('ARHGEF18', ['UniProtKB:A0A590UK10', 'UniProtKB:Q6ZSZ5']), ('ASIC5', ['UniProtKB:A0A0G2JLG4', 'UniProtKB:Q9NY37']), ('ATP6AP2', ['UniProtKB:O75787', 'UniProtKB:A0A1C7CYW4'])]\n"
     ]
    }
   ],
   "execution_count": 315
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:44:03.327073Z",
     "start_time": "2025-01-06T01:44:03.309006Z"
    }
   },
   "cell_type": "code",
   "source": "new_human",
   "id": "8d9cf08927c02bae",
   "outputs": [
    {
     "data": {
      "text/plain": [
       "                     subject subject_label    predicate      object  \\\n",
       "0       UniProtKB:A0A024RBG1        NUDT4B      enables  GO:0003723   \n",
       "1       UniProtKB:A0A024RBG1        NUDT4B      enables  GO:0005515   \n",
       "2       UniProtKB:A0A024RBG1        NUDT4B      enables  GO:0046872   \n",
       "3       UniProtKB:A0A024RBG1        NUDT4B   located_in  GO:0005829   \n",
       "4       UniProtKB:A0A075B6H5   TRBV20OR9-2  involved_in  GO:0002376   \n",
       "...                      ...           ...          ...         ...   \n",
       "434570      UniProtKB:Q9Y6A4        CFAP20         None  GO:0007275   \n",
       "435058      UniProtKB:Q9Y6F1         PARP3         None  GO:0006281   \n",
       "436209      UniProtKB:Q9Y6Q9         NCOA3         None  GO:0000981   \n",
       "436550      UniProtKB:Q9Y6X0        SETBP1         None  GO:0000981   \n",
       "436732      UniProtKB:Q9Y6Y1        CAMTA1         None  GO:0000981   \n",
       "\n",
       "                                             object_label  object_obsoletes  \\\n",
       "0                                             RNA binding             False   \n",
       "1                                         protein binding             False   \n",
       "2                                       metal ion binding             False   \n",
       "3                                                 cytosol             False   \n",
       "4                                   immune system process             False   \n",
       "...                                                   ...               ...   \n",
       "434570                 multicellular organism development             False   \n",
       "435058                                         DNA repair             False   \n",
       "436209  DNA-binding transcription factor activity, RNA...             False   \n",
       "436550  DNA-binding transcription factor activity, RNA...             False   \n",
       "436732  DNA-binding transcription factor activity, RNA...             False   \n",
       "\n",
       "        object_uninformative  \\\n",
       "0                       True   \n",
       "1                       True   \n",
       "2                       True   \n",
       "3                      False   \n",
       "4                      False   \n",
       "...                      ...   \n",
       "434570                  True   \n",
       "435058                 False   \n",
       "436209                 False   \n",
       "436550                 False   \n",
       "436732                 False   \n",
       "\n",
       "                                           object_closure  \\\n",
       "0       {GO:0097159, GO:0003723, BFO:0000015, GO:00036...   \n",
       "1       {BFO:0000015, GO:0003674, GO:0005488, BFO:0000...   \n",
       "2       {GO:0043169, GO:0046872, BFO:0000015, GO:00360...   \n",
       "3       {CARO:0030000, UBERON:0000061, CARO:0000003, G...   \n",
       "4       {GO:0008150, BFO:0000015, GO:0002376, BFO:0000...   \n",
       "...                                                   ...   \n",
       "434570  {GO:0032501, BFO:0000015, GO:0048856, GO:00325...   \n",
       "435058  {GO:0043170, GO:0033554, GO:0008152, GO:000613...   \n",
       "436209  {BFO:0000015, GO:0006357, GO:0008150, GO:00192...   \n",
       "436550  {BFO:0000015, GO:0006357, GO:0008150, GO:00192...   \n",
       "436732  {BFO:0000015, GO:0006357, GO:0008150, GO:00192...   \n",
       "\n",
       "                                 object_closure_redundant evidence  ...  \\\n",
       "0       {GO:0097159, BFO:0000015, GO:0003674, GO:00036...      IEA  ...   \n",
       "1       {GO:0003674, BFO:0000015, GO:0005488, BFO:0000...      IPI  ...   \n",
       "2       {GO:0043169, BFO:0000015, GO:0036094, GO:00431...      IEA  ...   \n",
       "3       {CARO:0030000, CARO:0000000, BFO:0000004, GO:0...      IDA  ...   \n",
       "4                  {BFO:0000015, GO:0008150, BFO:0000003}      IEA  ...   \n",
       "...                                                   ...      ...  ...   \n",
       "434570  {GO:0032501, BFO:0000015, GO:0048856, GO:00325...      TAS  ...   \n",
       "435058  {GO:0043170, GO:0008152, BFO:0000015, GO:00099...      TAS  ...   \n",
       "436209  {GO:0065007, GO:0060255, GO:0009889, BFO:00000...      ISM  ...   \n",
       "436550  {GO:0065007, GO:0060255, GO:0009889, BFO:00000...      ISM  ...   \n",
       "436732  {GO:0065007, GO:0060255, GO:0009889, BFO:00000...      ISM  ...   \n",
       "\n",
       "                    pubs     release pmid_new is_new  fresh pmid_removed  \\\n",
       "0       [GO_REF:0000043]  2024-11-03    False  False  False          NaN   \n",
       "1        [PMID:33961781]  2024-11-03     True   True   True          NaN   \n",
       "2       [GO_REF:0000043]  2024-11-03    False  False  False          NaN   \n",
       "3       [GO_REF:0000052]  2024-11-03    False  False  False          NaN   \n",
       "4       [GO_REF:0000043]  2024-11-03    False   True  False          NaN   \n",
       "...                  ...         ...      ...    ...    ...          ...   \n",
       "434570    [PMID:8688464]  2020-01-01      NaN    NaN    NaN         True   \n",
       "435058    [PMID:7260241]  2020-01-01      NaN    NaN    NaN         True   \n",
       "436209   [PMID:19274049]  2020-01-01      NaN    NaN    NaN         True   \n",
       "436550   [PMID:19274049]  2020-01-01      NaN    NaN    NaN         True   \n",
       "436732   [PMID:19274049]  2020-01-01      NaN    NaN    NaN         True   \n",
       "\n",
       "       unique redacted redundant iba_rejected  \n",
       "0         NaN      NaN     False         True  \n",
       "1         NaN      NaN     False         True  \n",
       "2         NaN      NaN     False         True  \n",
       "3         NaN      NaN     False         True  \n",
       "4         NaN      NaN     False         True  \n",
       "...       ...      ...       ...          ...  \n",
       "434570   True     True     False         True  \n",
       "435058   True     True      True        False  \n",
       "436209   True     True     False         True  \n",
       "436550   True     True     False         True  \n",
       "436732   True     True     False         True  \n",
       "\n",
       "[783918 rows x 23 columns]"
      ],
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>subject</th>\n",
       "      <th>subject_label</th>\n",
       "      <th>predicate</th>\n",
       "      <th>object</th>\n",
       "      <th>object_label</th>\n",
       "      <th>object_obsoletes</th>\n",
       "      <th>object_uninformative</th>\n",
       "      <th>object_closure</th>\n",
       "      <th>object_closure_redundant</th>\n",
       "      <th>evidence</th>\n",
       "      <th>...</th>\n",
       "      <th>pubs</th>\n",
       "      <th>release</th>\n",
       "      <th>pmid_new</th>\n",
       "      <th>is_new</th>\n",
       "      <th>fresh</th>\n",
       "      <th>pmid_removed</th>\n",
       "      <th>unique</th>\n",
       "      <th>redacted</th>\n",
       "      <th>redundant</th>\n",
       "      <th>iba_rejected</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>UniProtKB:A0A024RBG1</td>\n",
       "      <td>NUDT4B</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:0003723</td>\n",
       "      <td>RNA binding</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>{GO:0097159, GO:0003723, BFO:0000015, GO:00036...</td>\n",
       "      <td>{GO:0097159, BFO:0000015, GO:0003674, GO:00036...</td>\n",
       "      <td>IEA</td>\n",
       "      <td>...</td>\n",
       "      <td>[GO_REF:0000043]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>UniProtKB:A0A024RBG1</td>\n",
       "      <td>NUDT4B</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:0005515</td>\n",
       "      <td>protein binding</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>{BFO:0000015, GO:0003674, GO:0005488, BFO:0000...</td>\n",
       "      <td>{GO:0003674, BFO:0000015, GO:0005488, BFO:0000...</td>\n",
       "      <td>IPI</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:33961781]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>UniProtKB:A0A024RBG1</td>\n",
       "      <td>NUDT4B</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:0046872</td>\n",
       "      <td>metal ion binding</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>{GO:0043169, GO:0046872, BFO:0000015, GO:00360...</td>\n",
       "      <td>{GO:0043169, BFO:0000015, GO:0036094, GO:00431...</td>\n",
       "      <td>IEA</td>\n",
       "      <td>...</td>\n",
       "      <td>[GO_REF:0000043]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>UniProtKB:A0A024RBG1</td>\n",
       "      <td>NUDT4B</td>\n",
       "      <td>located_in</td>\n",
       "      <td>GO:0005829</td>\n",
       "      <td>cytosol</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{CARO:0030000, UBERON:0000061, CARO:0000003, G...</td>\n",
       "      <td>{CARO:0030000, CARO:0000000, BFO:0000004, GO:0...</td>\n",
       "      <td>IDA</td>\n",
       "      <td>...</td>\n",
       "      <td>[GO_REF:0000052]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>UniProtKB:A0A075B6H5</td>\n",
       "      <td>TRBV20OR9-2</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0002376</td>\n",
       "      <td>immune system process</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0008150, BFO:0000015, GO:0002376, BFO:0000...</td>\n",
       "      <td>{BFO:0000015, GO:0008150, BFO:0000003}</td>\n",
       "      <td>IEA</td>\n",
       "      <td>...</td>\n",
       "      <td>[GO_REF:0000043]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>434570</th>\n",
       "      <td>UniProtKB:Q9Y6A4</td>\n",
       "      <td>CFAP20</td>\n",
       "      <td>None</td>\n",
       "      <td>GO:0007275</td>\n",
       "      <td>multicellular organism development</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>{GO:0032501, BFO:0000015, GO:0048856, GO:00325...</td>\n",
       "      <td>{GO:0032501, BFO:0000015, GO:0048856, GO:00325...</td>\n",
       "      <td>TAS</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:8688464]</td>\n",
       "      <td>2020-01-01</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>435058</th>\n",
       "      <td>UniProtKB:Q9Y6F1</td>\n",
       "      <td>PARP3</td>\n",
       "      <td>None</td>\n",
       "      <td>GO:0006281</td>\n",
       "      <td>DNA repair</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0043170, GO:0033554, GO:0008152, GO:000613...</td>\n",
       "      <td>{GO:0043170, GO:0008152, BFO:0000015, GO:00099...</td>\n",
       "      <td>TAS</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:7260241]</td>\n",
       "      <td>2020-01-01</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>436209</th>\n",
       "      <td>UniProtKB:Q9Y6Q9</td>\n",
       "      <td>NCOA3</td>\n",
       "      <td>None</td>\n",
       "      <td>GO:0000981</td>\n",
       "      <td>DNA-binding transcription factor activity, RNA...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{BFO:0000015, GO:0006357, GO:0008150, GO:00192...</td>\n",
       "      <td>{GO:0065007, GO:0060255, GO:0009889, BFO:00000...</td>\n",
       "      <td>ISM</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:19274049]</td>\n",
       "      <td>2020-01-01</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>436550</th>\n",
       "      <td>UniProtKB:Q9Y6X0</td>\n",
       "      <td>SETBP1</td>\n",
       "      <td>None</td>\n",
       "      <td>GO:0000981</td>\n",
       "      <td>DNA-binding transcription factor activity, RNA...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{BFO:0000015, GO:0006357, GO:0008150, GO:00192...</td>\n",
       "      <td>{GO:0065007, GO:0060255, GO:0009889, BFO:00000...</td>\n",
       "      <td>ISM</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:19274049]</td>\n",
       "      <td>2020-01-01</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>436732</th>\n",
       "      <td>UniProtKB:Q9Y6Y1</td>\n",
       "      <td>CAMTA1</td>\n",
       "      <td>None</td>\n",
       "      <td>GO:0000981</td>\n",
       "      <td>DNA-binding transcription factor activity, RNA...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{BFO:0000015, GO:0006357, GO:0008150, GO:00192...</td>\n",
       "      <td>{GO:0065007, GO:0060255, GO:0009889, BFO:00000...</td>\n",
       "      <td>ISM</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:19274049]</td>\n",
       "      <td>2020-01-01</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>783918 rows × 23 columns</p>\n",
       "</div>"
      ]
     },
     "execution_count": 316,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "execution_count": 316
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:44:17.208851Z",
     "start_time": "2025-01-06T01:44:17.077948Z"
    }
   },
   "cell_type": "code",
   "source": "new_human[new_human['iba_rejected']]",
   "id": "171c5257a470dbee",
   "outputs": [
    {
     "data": {
      "text/plain": [
       "                     subject subject_label    predicate      object  \\\n",
       "0       UniProtKB:A0A024RBG1        NUDT4B      enables  GO:0003723   \n",
       "1       UniProtKB:A0A024RBG1        NUDT4B      enables  GO:0005515   \n",
       "2       UniProtKB:A0A024RBG1        NUDT4B      enables  GO:0046872   \n",
       "3       UniProtKB:A0A024RBG1        NUDT4B   located_in  GO:0005829   \n",
       "4       UniProtKB:A0A075B6H5   TRBV20OR9-2  involved_in  GO:0002376   \n",
       "...                      ...           ...          ...         ...   \n",
       "433680      UniProtKB:Q9Y5Y6          ST14         None  GO:0005887   \n",
       "434570      UniProtKB:Q9Y6A4        CFAP20         None  GO:0007275   \n",
       "436209      UniProtKB:Q9Y6Q9         NCOA3         None  GO:0000981   \n",
       "436550      UniProtKB:Q9Y6X0        SETBP1         None  GO:0000981   \n",
       "436732      UniProtKB:Q9Y6Y1        CAMTA1         None  GO:0000981   \n",
       "\n",
       "                                             object_label  object_obsoletes  \\\n",
       "0                                             RNA binding             False   \n",
       "1                                         protein binding             False   \n",
       "2                                       metal ion binding             False   \n",
       "3                                                 cytosol             False   \n",
       "4                                   immune system process             False   \n",
       "...                                                   ...               ...   \n",
       "433680                                               None              True   \n",
       "434570                 multicellular organism development             False   \n",
       "436209  DNA-binding transcription factor activity, RNA...             False   \n",
       "436550  DNA-binding transcription factor activity, RNA...             False   \n",
       "436732  DNA-binding transcription factor activity, RNA...             False   \n",
       "\n",
       "        object_uninformative  \\\n",
       "0                       True   \n",
       "1                       True   \n",
       "2                       True   \n",
       "3                      False   \n",
       "4                      False   \n",
       "...                      ...   \n",
       "433680                 False   \n",
       "434570                  True   \n",
       "436209                 False   \n",
       "436550                 False   \n",
       "436732                 False   \n",
       "\n",
       "                                           object_closure  \\\n",
       "0       {GO:0097159, GO:0003723, BFO:0000015, GO:00036...   \n",
       "1       {BFO:0000015, GO:0003674, GO:0005488, BFO:0000...   \n",
       "2       {GO:0043169, GO:0046872, BFO:0000015, GO:00360...   \n",
       "3       {CARO:0030000, UBERON:0000061, CARO:0000003, G...   \n",
       "4       {GO:0008150, BFO:0000015, GO:0002376, BFO:0000...   \n",
       "...                                                   ...   \n",
       "433680                                       {GO:0005887}   \n",
       "434570  {GO:0032501, BFO:0000015, GO:0048856, GO:00325...   \n",
       "436209  {BFO:0000015, GO:0006357, GO:0008150, GO:00192...   \n",
       "436550  {BFO:0000015, GO:0006357, GO:0008150, GO:00192...   \n",
       "436732  {BFO:0000015, GO:0006357, GO:0008150, GO:00192...   \n",
       "\n",
       "                                 object_closure_redundant evidence  ...  \\\n",
       "0       {GO:0097159, BFO:0000015, GO:0003674, GO:00036...      IEA  ...   \n",
       "1       {GO:0003674, BFO:0000015, GO:0005488, BFO:0000...      IPI  ...   \n",
       "2       {GO:0043169, BFO:0000015, GO:0036094, GO:00431...      IEA  ...   \n",
       "3       {CARO:0030000, CARO:0000000, BFO:0000004, GO:0...      IDA  ...   \n",
       "4                  {BFO:0000015, GO:0008150, BFO:0000003}      IEA  ...   \n",
       "...                                                   ...      ...  ...   \n",
       "433680                                                 {}      TAS  ...   \n",
       "434570  {GO:0032501, BFO:0000015, GO:0048856, GO:00325...      TAS  ...   \n",
       "436209  {GO:0065007, GO:0060255, GO:0009889, BFO:00000...      ISM  ...   \n",
       "436550  {GO:0065007, GO:0060255, GO:0009889, BFO:00000...      ISM  ...   \n",
       "436732  {GO:0065007, GO:0060255, GO:0009889, BFO:00000...      ISM  ...   \n",
       "\n",
       "                    pubs     release pmid_new is_new  fresh pmid_removed  \\\n",
       "0       [GO_REF:0000043]  2024-11-03    False  False  False          NaN   \n",
       "1        [PMID:33961781]  2024-11-03     True   True   True          NaN   \n",
       "2       [GO_REF:0000043]  2024-11-03    False  False  False          NaN   \n",
       "3       [GO_REF:0000052]  2024-11-03    False  False  False          NaN   \n",
       "4       [GO_REF:0000043]  2024-11-03    False   True  False          NaN   \n",
       "...                  ...         ...      ...    ...    ...          ...   \n",
       "433680   [PMID:10831593]  2020-01-01      NaN    NaN    NaN         True   \n",
       "434570    [PMID:8688464]  2020-01-01      NaN    NaN    NaN         True   \n",
       "436209   [PMID:19274049]  2020-01-01      NaN    NaN    NaN         True   \n",
       "436550   [PMID:19274049]  2020-01-01      NaN    NaN    NaN         True   \n",
       "436732   [PMID:19274049]  2020-01-01      NaN    NaN    NaN         True   \n",
       "\n",
       "       unique redacted redundant iba_rejected  \n",
       "0         NaN      NaN     False         True  \n",
       "1         NaN      NaN     False         True  \n",
       "2         NaN      NaN     False         True  \n",
       "3         NaN      NaN     False         True  \n",
       "4         NaN      NaN     False         True  \n",
       "...       ...      ...       ...          ...  \n",
       "433680   True     True     False         True  \n",
       "434570   True     True     False         True  \n",
       "436209   True     True     False         True  \n",
       "436550   True     True     False         True  \n",
       "436732   True     True     False         True  \n",
       "\n",
       "[450057 rows x 23 columns]"
      ],
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>subject</th>\n",
       "      <th>subject_label</th>\n",
       "      <th>predicate</th>\n",
       "      <th>object</th>\n",
       "      <th>object_label</th>\n",
       "      <th>object_obsoletes</th>\n",
       "      <th>object_uninformative</th>\n",
       "      <th>object_closure</th>\n",
       "      <th>object_closure_redundant</th>\n",
       "      <th>evidence</th>\n",
       "      <th>...</th>\n",
       "      <th>pubs</th>\n",
       "      <th>release</th>\n",
       "      <th>pmid_new</th>\n",
       "      <th>is_new</th>\n",
       "      <th>fresh</th>\n",
       "      <th>pmid_removed</th>\n",
       "      <th>unique</th>\n",
       "      <th>redacted</th>\n",
       "      <th>redundant</th>\n",
       "      <th>iba_rejected</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>UniProtKB:A0A024RBG1</td>\n",
       "      <td>NUDT4B</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:0003723</td>\n",
       "      <td>RNA binding</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>{GO:0097159, GO:0003723, BFO:0000015, GO:00036...</td>\n",
       "      <td>{GO:0097159, BFO:0000015, GO:0003674, GO:00036...</td>\n",
       "      <td>IEA</td>\n",
       "      <td>...</td>\n",
       "      <td>[GO_REF:0000043]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>UniProtKB:A0A024RBG1</td>\n",
       "      <td>NUDT4B</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:0005515</td>\n",
       "      <td>protein binding</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>{BFO:0000015, GO:0003674, GO:0005488, BFO:0000...</td>\n",
       "      <td>{GO:0003674, BFO:0000015, GO:0005488, BFO:0000...</td>\n",
       "      <td>IPI</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:33961781]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>UniProtKB:A0A024RBG1</td>\n",
       "      <td>NUDT4B</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:0046872</td>\n",
       "      <td>metal ion binding</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>{GO:0043169, GO:0046872, BFO:0000015, GO:00360...</td>\n",
       "      <td>{GO:0043169, BFO:0000015, GO:0036094, GO:00431...</td>\n",
       "      <td>IEA</td>\n",
       "      <td>...</td>\n",
       "      <td>[GO_REF:0000043]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>UniProtKB:A0A024RBG1</td>\n",
       "      <td>NUDT4B</td>\n",
       "      <td>located_in</td>\n",
       "      <td>GO:0005829</td>\n",
       "      <td>cytosol</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{CARO:0030000, UBERON:0000061, CARO:0000003, G...</td>\n",
       "      <td>{CARO:0030000, CARO:0000000, BFO:0000004, GO:0...</td>\n",
       "      <td>IDA</td>\n",
       "      <td>...</td>\n",
       "      <td>[GO_REF:0000052]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>UniProtKB:A0A075B6H5</td>\n",
       "      <td>TRBV20OR9-2</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0002376</td>\n",
       "      <td>immune system process</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0008150, BFO:0000015, GO:0002376, BFO:0000...</td>\n",
       "      <td>{BFO:0000015, GO:0008150, BFO:0000003}</td>\n",
       "      <td>IEA</td>\n",
       "      <td>...</td>\n",
       "      <td>[GO_REF:0000043]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>433680</th>\n",
       "      <td>UniProtKB:Q9Y5Y6</td>\n",
       "      <td>ST14</td>\n",
       "      <td>None</td>\n",
       "      <td>GO:0005887</td>\n",
       "      <td>None</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0005887}</td>\n",
       "      <td>{}</td>\n",
       "      <td>TAS</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:10831593]</td>\n",
       "      <td>2020-01-01</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>434570</th>\n",
       "      <td>UniProtKB:Q9Y6A4</td>\n",
       "      <td>CFAP20</td>\n",
       "      <td>None</td>\n",
       "      <td>GO:0007275</td>\n",
       "      <td>multicellular organism development</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>{GO:0032501, BFO:0000015, GO:0048856, GO:00325...</td>\n",
       "      <td>{GO:0032501, BFO:0000015, GO:0048856, GO:00325...</td>\n",
       "      <td>TAS</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:8688464]</td>\n",
       "      <td>2020-01-01</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>436209</th>\n",
       "      <td>UniProtKB:Q9Y6Q9</td>\n",
       "      <td>NCOA3</td>\n",
       "      <td>None</td>\n",
       "      <td>GO:0000981</td>\n",
       "      <td>DNA-binding transcription factor activity, RNA...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{BFO:0000015, GO:0006357, GO:0008150, GO:00192...</td>\n",
       "      <td>{GO:0065007, GO:0060255, GO:0009889, BFO:00000...</td>\n",
       "      <td>ISM</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:19274049]</td>\n",
       "      <td>2020-01-01</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>436550</th>\n",
       "      <td>UniProtKB:Q9Y6X0</td>\n",
       "      <td>SETBP1</td>\n",
       "      <td>None</td>\n",
       "      <td>GO:0000981</td>\n",
       "      <td>DNA-binding transcription factor activity, RNA...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{BFO:0000015, GO:0006357, GO:0008150, GO:00192...</td>\n",
       "      <td>{GO:0065007, GO:0060255, GO:0009889, BFO:00000...</td>\n",
       "      <td>ISM</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:19274049]</td>\n",
       "      <td>2020-01-01</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>436732</th>\n",
       "      <td>UniProtKB:Q9Y6Y1</td>\n",
       "      <td>CAMTA1</td>\n",
       "      <td>None</td>\n",
       "      <td>GO:0000981</td>\n",
       "      <td>DNA-binding transcription factor activity, RNA...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{BFO:0000015, GO:0006357, GO:0008150, GO:00192...</td>\n",
       "      <td>{GO:0065007, GO:0060255, GO:0009889, BFO:00000...</td>\n",
       "      <td>ISM</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:19274049]</td>\n",
       "      <td>2020-01-01</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>450057 rows × 23 columns</p>\n",
       "</div>"
      ]
     },
     "execution_count": 317,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "execution_count": 317
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:47:20.371960Z",
     "start_time": "2025-01-06T01:44:26.950777Z"
    }
   },
   "cell_type": "code",
   "source": [
    "prev_human_df = assocs_to_df(db[\"goa_human\"][PREVIOUS[0]], PREVIOUS[0])\n",
    "#annotate_new_pubs(human_df, prev_human_df)"
   ],
   "id": "14737ac8286733a5",
   "outputs": [],
   "execution_count": 318
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:47:44.842883Z",
     "start_time": "2025-01-06T01:47:34.278374Z"
    }
   },
   "cell_type": "code",
   "source": "annotate_new_pubs(human_df, prev_human_df)",
   "id": "3a4124cdc8a825f4",
   "outputs": [],
   "execution_count": 319
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:47:44.893482Z",
     "start_time": "2025-01-06T01:47:44.874646Z"
    }
   },
   "cell_type": "code",
   "source": "human_df[human_df['fresh']]",
   "id": "4283533cfc17e67c",
   "outputs": [
    {
     "data": {
      "text/plain": [
       "                              subject       subject_label    predicate  \\\n",
       "1                UniProtKB:A0A024RBG1              NUDT4B      enables   \n",
       "357              UniProtKB:A0A096LP55              UQCRHL   located_in   \n",
       "569              UniProtKB:A0A0B4J2F0             PIGBOS1   located_in   \n",
       "1904                 UniProtKB:A1A4Y4                IRGM      enables   \n",
       "1945                 UniProtKB:A1A4Y4                IRGM  involved_in   \n",
       "...                               ...                 ...          ...   \n",
       "718365  RNAcentral:URS00026A23F2_9606  URS00026A23F2_9606      enables   \n",
       "718366  RNAcentral:URS00026A23F2_9606  URS00026A23F2_9606  involved_in   \n",
       "718367  RNAcentral:URS00026A23F2_9606  URS00026A23F2_9606  involved_in   \n",
       "718368  RNAcentral:URS00026A23F2_9606  URS00026A23F2_9606  involved_in   \n",
       "718370  RNAcentral:URS00026A23F2_9606  URS00026A23F2_9606  involved_in   \n",
       "\n",
       "            object                                       object_label  \\\n",
       "1       GO:0005515                                    protein binding   \n",
       "357     GO:0005739                                      mitochondrion   \n",
       "569     GO:0005739                                      mitochondrion   \n",
       "1904    GO:1901612                                cardiolipin binding   \n",
       "1945    GO:0090141       positive regulation of mitochondrial fission   \n",
       "...            ...                                                ...   \n",
       "718365  GO:0141180  dsDNA-RNA triple helix-forming chromatin adapt...   \n",
       "718366  GO:0000122  negative regulation of transcription by RNA po...   \n",
       "718367  GO:0000512  lncRNA-mediated post-transcriptional gene sile...   \n",
       "718368  GO:0000512  lncRNA-mediated post-transcriptional gene sile...   \n",
       "718370  GO:0090399                             replicative senescence   \n",
       "\n",
       "        object_obsoletes  object_uninformative  \\\n",
       "1                  False                  True   \n",
       "357                False                 False   \n",
       "569                False                 False   \n",
       "1904               False                  True   \n",
       "1945               False                 False   \n",
       "...                  ...                   ...   \n",
       "718365             False                  True   \n",
       "718366             False                 False   \n",
       "718367             False                 False   \n",
       "718368             False                 False   \n",
       "718370             False                 False   \n",
       "\n",
       "                                           object_closure  \\\n",
       "1       {BFO:0000015, GO:0003674, GO:0005488, BFO:0000...   \n",
       "357     {GO:0005739, GO:0110165, GO:0043231, BFO:00000...   \n",
       "569     {GO:0005739, GO:0110165, GO:0043231, BFO:00000...   \n",
       "1904    {GO:0008289, GO:0043168, GO:1901612, BFO:00000...   \n",
       "1945    {GO:0010821, GO:0051130, GO:0065007, GO:003304...   \n",
       "...                                                   ...   \n",
       "718365  {GO:0030674, BFO:0000015, GO:0043565, GO:00036...   \n",
       "718366  {BFO:0000015, GO:0006357, GO:0008150, GO:00098...   \n",
       "718367  {GO:0000512, BFO:0000015, GO:0016441, GO:00081...   \n",
       "718368  {GO:0000512, BFO:0000015, GO:0016441, GO:00081...   \n",
       "718370  {GO:0008152, BFO:0000015, GO:0090399, GO:00099...   \n",
       "\n",
       "                                 object_closure_redundant evidence  is_iba  \\\n",
       "1       {GO:0003674, BFO:0000015, GO:0005488, BFO:0000...      IPI   False   \n",
       "357     {CARO:0030000, CARO:0000000, BFO:0000004, GO:0...      HTP   False   \n",
       "569     {CARO:0030000, CARO:0000000, BFO:0000004, GO:0...      HTP   False   \n",
       "1904    {GO:0008289, GO:0043168, BFO:0000015, GO:00360...      IDA   False   \n",
       "1945    {GO:0010821, GO:0051130, GO:0065007, GO:003304...      IDA   False   \n",
       "...                                                   ...      ...     ...   \n",
       "718365  {GO:0003690, GO:0030674, GO:0003677, GO:007184...      IDA   False   \n",
       "718366  {GO:0045934, GO:0009892, GO:0065007, GO:000988...      IMP   False   \n",
       "718367  {GO:0065007, GO:0009892, GO:0031047, GO:000988...      IDA   False   \n",
       "718368  {GO:0065007, GO:0009892, GO:0031047, GO:000988...      IMP   False   \n",
       "718370  {GO:0008152, BFO:0000015, GO:0009987, GO:00081...      IMP   False   \n",
       "\n",
       "       negated           pmid             pubs     release  pmid_new  is_new  \\\n",
       "1         None  PMID:33961781  [PMID:33961781]  2024-11-03      True    True   \n",
       "357       None  PMID:34800366  [PMID:34800366]  2024-11-03      True    True   \n",
       "569       None  PMID:34800366  [PMID:34800366]  2024-11-03      True    True   \n",
       "1904      None  PMID:21102437  [PMID:21102437]  2024-11-03      True    True   \n",
       "1945      None  PMID:21102437  [PMID:21102437]  2024-11-03      True    True   \n",
       "...        ...            ...              ...         ...       ...     ...   \n",
       "718365    None  PMID:27634931  [PMID:27634931]  2024-11-03      True    True   \n",
       "718366    None  PMID:27634931  [PMID:27634931]  2024-11-03      True    True   \n",
       "718367    None  PMID:30720199  [PMID:30720199]  2024-11-03      True    True   \n",
       "718368    None  PMID:33102210  [PMID:33102210]  2024-11-03      True    True   \n",
       "718370    None  PMID:27634931  [PMID:27634931]  2024-11-03      True    True   \n",
       "\n",
       "        fresh  \n",
       "1        True  \n",
       "357      True  \n",
       "569      True  \n",
       "1904     True  \n",
       "1945     True  \n",
       "...       ...  \n",
       "718365   True  \n",
       "718366   True  \n",
       "718367   True  \n",
       "718368   True  \n",
       "718370   True  \n",
       "\n",
       "[3380 rows x 18 columns]"
      ],
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>subject</th>\n",
       "      <th>subject_label</th>\n",
       "      <th>predicate</th>\n",
       "      <th>object</th>\n",
       "      <th>object_label</th>\n",
       "      <th>object_obsoletes</th>\n",
       "      <th>object_uninformative</th>\n",
       "      <th>object_closure</th>\n",
       "      <th>object_closure_redundant</th>\n",
       "      <th>evidence</th>\n",
       "      <th>is_iba</th>\n",
       "      <th>negated</th>\n",
       "      <th>pmid</th>\n",
       "      <th>pubs</th>\n",
       "      <th>release</th>\n",
       "      <th>pmid_new</th>\n",
       "      <th>is_new</th>\n",
       "      <th>fresh</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>UniProtKB:A0A024RBG1</td>\n",
       "      <td>NUDT4B</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:0005515</td>\n",
       "      <td>protein binding</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>{BFO:0000015, GO:0003674, GO:0005488, BFO:0000...</td>\n",
       "      <td>{GO:0003674, BFO:0000015, GO:0005488, BFO:0000...</td>\n",
       "      <td>IPI</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:33961781</td>\n",
       "      <td>[PMID:33961781]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>357</th>\n",
       "      <td>UniProtKB:A0A096LP55</td>\n",
       "      <td>UQCRHL</td>\n",
       "      <td>located_in</td>\n",
       "      <td>GO:0005739</td>\n",
       "      <td>mitochondrion</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0005739, GO:0110165, GO:0043231, BFO:00000...</td>\n",
       "      <td>{CARO:0030000, CARO:0000000, BFO:0000004, GO:0...</td>\n",
       "      <td>HTP</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:34800366</td>\n",
       "      <td>[PMID:34800366]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>569</th>\n",
       "      <td>UniProtKB:A0A0B4J2F0</td>\n",
       "      <td>PIGBOS1</td>\n",
       "      <td>located_in</td>\n",
       "      <td>GO:0005739</td>\n",
       "      <td>mitochondrion</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0005739, GO:0110165, GO:0043231, BFO:00000...</td>\n",
       "      <td>{CARO:0030000, CARO:0000000, BFO:0000004, GO:0...</td>\n",
       "      <td>HTP</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:34800366</td>\n",
       "      <td>[PMID:34800366]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1904</th>\n",
       "      <td>UniProtKB:A1A4Y4</td>\n",
       "      <td>IRGM</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:1901612</td>\n",
       "      <td>cardiolipin binding</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>{GO:0008289, GO:0043168, GO:1901612, BFO:00000...</td>\n",
       "      <td>{GO:0008289, GO:0043168, BFO:0000015, GO:00360...</td>\n",
       "      <td>IDA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:21102437</td>\n",
       "      <td>[PMID:21102437]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1945</th>\n",
       "      <td>UniProtKB:A1A4Y4</td>\n",
       "      <td>IRGM</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0090141</td>\n",
       "      <td>positive regulation of mitochondrial fission</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0010821, GO:0051130, GO:0065007, GO:003304...</td>\n",
       "      <td>{GO:0010821, GO:0051130, GO:0065007, GO:003304...</td>\n",
       "      <td>IDA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:21102437</td>\n",
       "      <td>[PMID:21102437]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>718365</th>\n",
       "      <td>RNAcentral:URS00026A23F2_9606</td>\n",
       "      <td>URS00026A23F2_9606</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:0141180</td>\n",
       "      <td>dsDNA-RNA triple helix-forming chromatin adapt...</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>{GO:0030674, BFO:0000015, GO:0043565, GO:00036...</td>\n",
       "      <td>{GO:0003690, GO:0030674, GO:0003677, GO:007184...</td>\n",
       "      <td>IDA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:27634931</td>\n",
       "      <td>[PMID:27634931]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>718366</th>\n",
       "      <td>RNAcentral:URS00026A23F2_9606</td>\n",
       "      <td>URS00026A23F2_9606</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0000122</td>\n",
       "      <td>negative regulation of transcription by RNA po...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{BFO:0000015, GO:0006357, GO:0008150, GO:00098...</td>\n",
       "      <td>{GO:0045934, GO:0009892, GO:0065007, GO:000988...</td>\n",
       "      <td>IMP</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:27634931</td>\n",
       "      <td>[PMID:27634931]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>718367</th>\n",
       "      <td>RNAcentral:URS00026A23F2_9606</td>\n",
       "      <td>URS00026A23F2_9606</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0000512</td>\n",
       "      <td>lncRNA-mediated post-transcriptional gene sile...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0000512, BFO:0000015, GO:0016441, GO:00081...</td>\n",
       "      <td>{GO:0065007, GO:0009892, GO:0031047, GO:000988...</td>\n",
       "      <td>IDA</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:30720199</td>\n",
       "      <td>[PMID:30720199]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>718368</th>\n",
       "      <td>RNAcentral:URS00026A23F2_9606</td>\n",
       "      <td>URS00026A23F2_9606</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0000512</td>\n",
       "      <td>lncRNA-mediated post-transcriptional gene sile...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0000512, BFO:0000015, GO:0016441, GO:00081...</td>\n",
       "      <td>{GO:0065007, GO:0009892, GO:0031047, GO:000988...</td>\n",
       "      <td>IMP</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:33102210</td>\n",
       "      <td>[PMID:33102210]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>718370</th>\n",
       "      <td>RNAcentral:URS00026A23F2_9606</td>\n",
       "      <td>URS00026A23F2_9606</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0090399</td>\n",
       "      <td>replicative senescence</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0008152, BFO:0000015, GO:0090399, GO:00099...</td>\n",
       "      <td>{GO:0008152, BFO:0000015, GO:0009987, GO:00081...</td>\n",
       "      <td>IMP</td>\n",
       "      <td>False</td>\n",
       "      <td>None</td>\n",
       "      <td>PMID:27634931</td>\n",
       "      <td>[PMID:27634931]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>3380 rows × 18 columns</p>\n",
       "</div>"
      ]
     },
     "execution_count": 320,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "execution_count": 320
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:47:58.760497Z",
     "start_time": "2025-01-06T01:47:58.758393Z"
    }
   },
   "cell_type": "code",
   "source": "#pair_assocs, pair_anns = annotate_assocs(\"tair\")",
   "id": "35e6ea6ce6f45958",
   "outputs": [],
   "execution_count": 321
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T01:48:10.671121Z",
     "start_time": "2025-01-06T01:47:58.773655Z"
    }
   },
   "cell_type": "code",
   "source": "new_human.to_csv(\"output/go-human-assocs-annotated.csv\", index=False)",
   "id": "98d63328995a6be1",
   "outputs": [],
   "execution_count": 322
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T02:28:43.837036Z",
     "start_time": "2025-01-06T02:28:43.768532Z"
    }
   },
   "cell_type": "code",
   "source": [
    "test_cases_df = new_human[(new_human['fresh'] == True) & (new_human['object_uninformative'] == False) & (new_human['negated'] != True) & (new_human['redundant'] != True) & (new_human['iba_rejected'] != True)]\n",
    "test_cases_df"
   ],
   "id": "292a3fc05eafeb5f",
   "outputs": [
    {
     "data": {
      "text/plain": [
       "                              subject       subject_label         predicate  \\\n",
       "4876                 UniProtKB:A6NNL5            C15orf61        located_in   \n",
       "5853                 UniProtKB:A8MSI8               LYRM9        located_in   \n",
       "6327                 UniProtKB:A8MXV4              NUDT19        located_in   \n",
       "15942                UniProtKB:O14521                SDHD           part_of   \n",
       "34482                UniProtKB:O43325               LYRM1        located_in   \n",
       "...                               ...                 ...               ...   \n",
       "718362  RNAcentral:URS00026A23F2_9606  URS00026A23F2_9606  acts_upstream_of   \n",
       "718366  RNAcentral:URS00026A23F2_9606  URS00026A23F2_9606       involved_in   \n",
       "718367  RNAcentral:URS00026A23F2_9606  URS00026A23F2_9606       involved_in   \n",
       "718368  RNAcentral:URS00026A23F2_9606  URS00026A23F2_9606       involved_in   \n",
       "718370  RNAcentral:URS00026A23F2_9606  URS00026A23F2_9606       involved_in   \n",
       "\n",
       "            object                                       object_label  \\\n",
       "4876    GO:0005739                                      mitochondrion   \n",
       "5853    GO:0005739                                      mitochondrion   \n",
       "6327    GO:0005739                                      mitochondrion   \n",
       "15942   GO:0045273  respiratory chain complex II (succinate dehydr...   \n",
       "34482   GO:0005739                                      mitochondrion   \n",
       "...            ...                                                ...   \n",
       "718362  GO:0008284  positive regulation of cell population prolife...   \n",
       "718366  GO:0000122  negative regulation of transcription by RNA po...   \n",
       "718367  GO:0000512  lncRNA-mediated post-transcriptional gene sile...   \n",
       "718368  GO:0000512  lncRNA-mediated post-transcriptional gene sile...   \n",
       "718370  GO:0090399                             replicative senescence   \n",
       "\n",
       "        object_obsoletes  object_uninformative  \\\n",
       "4876               False                 False   \n",
       "5853               False                 False   \n",
       "6327               False                 False   \n",
       "15942              False                 False   \n",
       "34482              False                 False   \n",
       "...                  ...                   ...   \n",
       "718362             False                 False   \n",
       "718366             False                 False   \n",
       "718367             False                 False   \n",
       "718368             False                 False   \n",
       "718370             False                 False   \n",
       "\n",
       "                                           object_closure  \\\n",
       "4876    {GO:0005739, GO:0110165, GO:0043231, BFO:00000...   \n",
       "5853    {GO:0005739, GO:0110165, GO:0043231, BFO:00000...   \n",
       "6327    {GO:0005739, GO:0110165, GO:0043231, BFO:00000...   \n",
       "15942   {GO:0098796, GO:0110165, GO:0045273, BFO:00000...   \n",
       "34482   {GO:0005739, GO:0110165, GO:0043231, BFO:00000...   \n",
       "...                                                   ...   \n",
       "718362  {GO:0065007, GO:0042127, GO:0048518, BFO:00000...   \n",
       "718366  {BFO:0000015, GO:0006357, GO:0008150, GO:00098...   \n",
       "718367  {GO:0000512, BFO:0000015, GO:0016441, GO:00081...   \n",
       "718368  {GO:0000512, BFO:0000015, GO:0016441, GO:00081...   \n",
       "718370  {GO:0008152, BFO:0000015, GO:0090399, GO:00099...   \n",
       "\n",
       "                                 object_closure_redundant evidence  ...  \\\n",
       "4876    {CARO:0030000, CARO:0000000, BFO:0000004, GO:0...      HTP  ...   \n",
       "5853    {CARO:0030000, CARO:0000000, BFO:0000004, GO:0...      HTP  ...   \n",
       "6327    {CARO:0030000, CARO:0000000, BFO:0000004, GO:0...      HTP  ...   \n",
       "15942   {CARO:0030000, GO:0098803, GO:0098796, CARO:00...      IDA  ...   \n",
       "34482   {CARO:0030000, CARO:0000000, BFO:0000004, GO:0...      HTP  ...   \n",
       "...                                                   ...      ...  ...   \n",
       "718362  {GO:0065007, GO:0042127, GO:0048518, BFO:00000...      IMP  ...   \n",
       "718366  {GO:0045934, GO:0009892, GO:0065007, GO:000988...      IMP  ...   \n",
       "718367  {GO:0065007, GO:0009892, GO:0031047, GO:000988...      IDA  ...   \n",
       "718368  {GO:0065007, GO:0009892, GO:0031047, GO:000988...      IMP  ...   \n",
       "718370  {GO:0008152, BFO:0000015, GO:0009987, GO:00081...      IMP  ...   \n",
       "\n",
       "                   pubs     release pmid_new is_new fresh pmid_removed unique  \\\n",
       "4876    [PMID:34800366]  2024-11-03     True   True  True          NaN    NaN   \n",
       "5853    [PMID:34800366]  2024-11-03     True   True  True          NaN    NaN   \n",
       "6327    [PMID:34800366]  2024-11-03     True   True  True          NaN    NaN   \n",
       "15942   [PMID:37098072]  2024-11-03     True   True  True          NaN    NaN   \n",
       "34482   [PMID:34800366]  2024-11-03     True   True  True          NaN    NaN   \n",
       "...                 ...         ...      ...    ...   ...          ...    ...   \n",
       "718362  [PMID:33102210]  2024-11-03     True   True  True          NaN    NaN   \n",
       "718366  [PMID:27634931]  2024-11-03     True   True  True          NaN    NaN   \n",
       "718367  [PMID:30720199]  2024-11-03     True   True  True          NaN    NaN   \n",
       "718368  [PMID:33102210]  2024-11-03     True   True  True          NaN    NaN   \n",
       "718370  [PMID:27634931]  2024-11-03     True   True  True          NaN    NaN   \n",
       "\n",
       "       redacted redundant iba_rejected  \n",
       "4876        NaN     False        False  \n",
       "5853        NaN     False        False  \n",
       "6327        NaN     False        False  \n",
       "15942       NaN     False        False  \n",
       "34482       NaN     False        False  \n",
       "...         ...       ...          ...  \n",
       "718362      NaN     False        False  \n",
       "718366      NaN     False        False  \n",
       "718367      NaN     False        False  \n",
       "718368      NaN     False        False  \n",
       "718370      NaN     False        False  \n",
       "\n",
       "[524 rows x 23 columns]"
      ],
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>subject</th>\n",
       "      <th>subject_label</th>\n",
       "      <th>predicate</th>\n",
       "      <th>object</th>\n",
       "      <th>object_label</th>\n",
       "      <th>object_obsoletes</th>\n",
       "      <th>object_uninformative</th>\n",
       "      <th>object_closure</th>\n",
       "      <th>object_closure_redundant</th>\n",
       "      <th>evidence</th>\n",
       "      <th>...</th>\n",
       "      <th>pubs</th>\n",
       "      <th>release</th>\n",
       "      <th>pmid_new</th>\n",
       "      <th>is_new</th>\n",
       "      <th>fresh</th>\n",
       "      <th>pmid_removed</th>\n",
       "      <th>unique</th>\n",
       "      <th>redacted</th>\n",
       "      <th>redundant</th>\n",
       "      <th>iba_rejected</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>4876</th>\n",
       "      <td>UniProtKB:A6NNL5</td>\n",
       "      <td>C15orf61</td>\n",
       "      <td>located_in</td>\n",
       "      <td>GO:0005739</td>\n",
       "      <td>mitochondrion</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0005739, GO:0110165, GO:0043231, BFO:00000...</td>\n",
       "      <td>{CARO:0030000, CARO:0000000, BFO:0000004, GO:0...</td>\n",
       "      <td>HTP</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:34800366]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5853</th>\n",
       "      <td>UniProtKB:A8MSI8</td>\n",
       "      <td>LYRM9</td>\n",
       "      <td>located_in</td>\n",
       "      <td>GO:0005739</td>\n",
       "      <td>mitochondrion</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0005739, GO:0110165, GO:0043231, BFO:00000...</td>\n",
       "      <td>{CARO:0030000, CARO:0000000, BFO:0000004, GO:0...</td>\n",
       "      <td>HTP</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:34800366]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6327</th>\n",
       "      <td>UniProtKB:A8MXV4</td>\n",
       "      <td>NUDT19</td>\n",
       "      <td>located_in</td>\n",
       "      <td>GO:0005739</td>\n",
       "      <td>mitochondrion</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0005739, GO:0110165, GO:0043231, BFO:00000...</td>\n",
       "      <td>{CARO:0030000, CARO:0000000, BFO:0000004, GO:0...</td>\n",
       "      <td>HTP</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:34800366]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15942</th>\n",
       "      <td>UniProtKB:O14521</td>\n",
       "      <td>SDHD</td>\n",
       "      <td>part_of</td>\n",
       "      <td>GO:0045273</td>\n",
       "      <td>respiratory chain complex II (succinate dehydr...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0098796, GO:0110165, GO:0045273, BFO:00000...</td>\n",
       "      <td>{CARO:0030000, GO:0098803, GO:0098796, CARO:00...</td>\n",
       "      <td>IDA</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:37098072]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34482</th>\n",
       "      <td>UniProtKB:O43325</td>\n",
       "      <td>LYRM1</td>\n",
       "      <td>located_in</td>\n",
       "      <td>GO:0005739</td>\n",
       "      <td>mitochondrion</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0005739, GO:0110165, GO:0043231, BFO:00000...</td>\n",
       "      <td>{CARO:0030000, CARO:0000000, BFO:0000004, GO:0...</td>\n",
       "      <td>HTP</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:34800366]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>718362</th>\n",
       "      <td>RNAcentral:URS00026A23F2_9606</td>\n",
       "      <td>URS00026A23F2_9606</td>\n",
       "      <td>acts_upstream_of</td>\n",
       "      <td>GO:0008284</td>\n",
       "      <td>positive regulation of cell population prolife...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0065007, GO:0042127, GO:0048518, BFO:00000...</td>\n",
       "      <td>{GO:0065007, GO:0042127, GO:0048518, BFO:00000...</td>\n",
       "      <td>IMP</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:33102210]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>718366</th>\n",
       "      <td>RNAcentral:URS00026A23F2_9606</td>\n",
       "      <td>URS00026A23F2_9606</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0000122</td>\n",
       "      <td>negative regulation of transcription by RNA po...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{BFO:0000015, GO:0006357, GO:0008150, GO:00098...</td>\n",
       "      <td>{GO:0045934, GO:0009892, GO:0065007, GO:000988...</td>\n",
       "      <td>IMP</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:27634931]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>718367</th>\n",
       "      <td>RNAcentral:URS00026A23F2_9606</td>\n",
       "      <td>URS00026A23F2_9606</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0000512</td>\n",
       "      <td>lncRNA-mediated post-transcriptional gene sile...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0000512, BFO:0000015, GO:0016441, GO:00081...</td>\n",
       "      <td>{GO:0065007, GO:0009892, GO:0031047, GO:000988...</td>\n",
       "      <td>IDA</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:30720199]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>718368</th>\n",
       "      <td>RNAcentral:URS00026A23F2_9606</td>\n",
       "      <td>URS00026A23F2_9606</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0000512</td>\n",
       "      <td>lncRNA-mediated post-transcriptional gene sile...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0000512, BFO:0000015, GO:0016441, GO:00081...</td>\n",
       "      <td>{GO:0065007, GO:0009892, GO:0031047, GO:000988...</td>\n",
       "      <td>IMP</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:33102210]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>718370</th>\n",
       "      <td>RNAcentral:URS00026A23F2_9606</td>\n",
       "      <td>URS00026A23F2_9606</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0090399</td>\n",
       "      <td>replicative senescence</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0008152, BFO:0000015, GO:0090399, GO:00099...</td>\n",
       "      <td>{GO:0008152, BFO:0000015, GO:0009987, GO:00081...</td>\n",
       "      <td>IMP</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:27634931]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>524 rows × 23 columns</p>\n",
       "</div>"
      ]
     },
     "execution_count": 332,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "execution_count": 332
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T16:39:16.785481Z",
     "start_time": "2025-01-06T16:39:16.748334Z"
    }
   },
   "cell_type": "code",
   "source": [
    "def row_to_test_case(row, answer=\"YES\"):\n",
    "    gene = row['subject_label']\n",
    "    term = row['object_label']\n",
    "    predicate = row['predicate']\n",
    "    if not gene or not term or not predicate:\n",
    "        return\n",
    "    \n",
    "    return {\n",
    "        \"input\": f\"{gene} {predicate} {term}\",\n",
    "        \"original_input\": {\n",
    "            \"subject\": str(row['subject']),\n",
    "            \"predicate\": str(row['predicate']),\n",
    "            \"object\": str(row['object']),\n",
    "        },\n",
    "        \"ideal\": answer,\n",
    "    }\n",
    "\n",
    "\n",
    "def df_to_test_cases(df: pd.DataFrame, limit=1000):\n",
    "    cases = [row_to_test_case(row) for _, row in df.iterrows()]\n",
    "    cases = [x for x in cases if x is not None]\n",
    "    if limit:\n",
    "        cases = cases[:limit]\n",
    "    return cases\n",
    "\n",
    "df_to_test_cases(test_cases_df, limit=5)"
   ],
   "id": "ef5c09fd349f7646",
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[{'input': 'C15orf61 located_in mitochondrion',\n",
       "  'original_input': {'subject': 'UniProtKB:A6NNL5',\n",
       "   'predicate': 'located_in',\n",
       "   'object': 'GO:0005739'},\n",
       "  'ideal': 'YES'},\n",
       " {'input': 'LYRM9 located_in mitochondrion',\n",
       "  'original_input': {'subject': 'UniProtKB:A8MSI8',\n",
       "   'predicate': 'located_in',\n",
       "   'object': 'GO:0005739'},\n",
       "  'ideal': 'YES'},\n",
       " {'input': 'NUDT19 located_in mitochondrion',\n",
       "  'original_input': {'subject': 'UniProtKB:A8MXV4',\n",
       "   'predicate': 'located_in',\n",
       "   'object': 'GO:0005739'},\n",
       "  'ideal': 'YES'},\n",
       " {'input': 'SDHD part_of respiratory chain complex II (succinate dehydrogenase)',\n",
       "  'original_input': {'subject': 'UniProtKB:O14521',\n",
       "   'predicate': 'part_of',\n",
       "   'object': 'GO:0045273'},\n",
       "  'ideal': 'YES'},\n",
       " {'input': 'LYRM1 located_in mitochondrion',\n",
       "  'original_input': {'subject': 'UniProtKB:O43325',\n",
       "   'predicate': 'located_in',\n",
       "   'object': 'GO:0005739'},\n",
       "  'ideal': 'YES'}]"
      ]
     },
     "execution_count": 350,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "execution_count": 350
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T02:34:40.733465Z",
     "start_time": "2025-01-06T02:34:40.706998Z"
    }
   },
   "cell_type": "code",
   "source": "#cases = [row_to_test_case(row) for _, row in test_cases_df.iterrows()]\n",
   "id": "db505d632ca52fde",
   "outputs": [],
   "execution_count": 341
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T02:35:09.227224Z",
     "start_time": "2025-01-06T02:35:09.064306Z"
    }
   },
   "cell_type": "code",
   "source": [
    "import yaml\n",
    "\n",
    "with open(\"output/test-cases.yaml\", \"w\") as f:\n",
    "    yaml.dump({\"cases\": cases}, f, sort_keys=False)"
   ],
   "id": "43a7fc62e139e2a8",
   "outputs": [],
   "execution_count": 343
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T04:59:05.656278Z",
     "start_time": "2025-01-06T04:59:05.599644Z"
    }
   },
   "cell_type": "code",
   "source": [
    "redacted_df = new_human[(new_human['redacted'] == True) & (new_human['object_uninformative'] == False) & (new_human['negated'] != True) & (new_human['redundant'] != True) & (new_human['iba_rejected'] != True)]\n",
    "redacted_df"
   ],
   "id": "592aef9b9d45259a",
   "outputs": [
    {
     "data": {
      "text/plain": [
       "                              subject       subject_label    predicate  \\\n",
       "401144               UniProtKB:Q8N6R0             METTL13  involved_in   \n",
       "401146               UniProtKB:Q8N6R0             METTL13  involved_in   \n",
       "453842               UniProtKB:Q96K19              RNF170  involved_in   \n",
       "587451  RNAcentral:URS0000083D87_9606  URS0000083D87_9606  involved_in   \n",
       "587452  RNAcentral:URS0000083D87_9606  URS0000083D87_9606  involved_in   \n",
       "...                               ...                 ...          ...   \n",
       "424250               UniProtKB:Q9Y226            SLC22A13         None   \n",
       "425053               UniProtKB:Q9Y267            SLC22A14         None   \n",
       "425054               UniProtKB:Q9Y267            SLC22A14         None   \n",
       "425055               UniProtKB:Q9Y267            SLC22A14         None   \n",
       "432681               UniProtKB:Q9Y5M6                OCLM         None   \n",
       "\n",
       "            object                                       object_label  \\\n",
       "401144  GO:0000122  negative regulation of transcription by RNA po...   \n",
       "401146  GO:1902807  negative regulation of cell cycle G1/S phase t...   \n",
       "453842  GO:0034140  negative regulation of toll-like receptor 3 si...   \n",
       "587451  GO:0035195  miRNA-mediated post-transcriptional gene silen...   \n",
       "587452  GO:0090051  negative regulation of cell migration involved...   \n",
       "...            ...                                                ...   \n",
       "424250  GO:0015695                           organic cation transport   \n",
       "425053  GO:0005887                                               None   \n",
       "425054  GO:0015101  organic cation transmembrane transporter activity   \n",
       "425055  GO:0015695                           organic cation transport   \n",
       "432681  GO:0007601                                  visual perception   \n",
       "\n",
       "        object_obsoletes  object_uninformative  \\\n",
       "401144             False                 False   \n",
       "401146             False                 False   \n",
       "453842             False                 False   \n",
       "587451             False                 False   \n",
       "587452             False                 False   \n",
       "...                  ...                   ...   \n",
       "424250             False                 False   \n",
       "425053              True                 False   \n",
       "425054             False                 False   \n",
       "425055             False                 False   \n",
       "432681             False                 False   \n",
       "\n",
       "                                           object_closure  \\\n",
       "401144  {BFO:0000015, GO:0006357, GO:0008150, GO:00098...   \n",
       "401146  {GO:0065007, GO:1902806, GO:0010948, GO:190198...   \n",
       "453842  {GO:0048585, GO:0062207, GO:1902532, GO:000996...   \n",
       "587451  {BFO:0000015, GO:0016441, GO:0008150, GO:00106...   \n",
       "587452  {GO:0030336, BFO:0000015, GO:0008150, GO:00105...   \n",
       "...                                                   ...   \n",
       "424250  {GO:0051234, GO:0006810, BFO:0000015, GO:00156...   \n",
       "425053                                       {GO:0005887}   \n",
       "425054  {GO:0051234, GO:0055085, GO:0006810, BFO:00000...   \n",
       "425055  {GO:0051234, GO:0006810, BFO:0000015, GO:00156...   \n",
       "432681  {GO:0032501, GO:0050953, GO:0003008, BFO:00000...   \n",
       "\n",
       "                                 object_closure_redundant evidence  ...  \\\n",
       "401144  {GO:0045934, GO:0009892, GO:0065007, GO:000988...      IMP  ...   \n",
       "401146  {GO:0065007, GO:0010948, GO:1901988, GO:005172...      IMP  ...   \n",
       "453842  {GO:0048585, GO:0065007, GO:0002682, GO:006220...      IDA  ...   \n",
       "587451  {GO:0065007, GO:0009892, GO:0031047, GO:000988...      IDA  ...   \n",
       "587452  {GO:0065007, GO:0030336, BFO:0000015, GO:00485...      IGI  ...   \n",
       "...                                                   ...      ...  ...   \n",
       "424250  {GO:0051234, GO:0006810, BFO:0000015, GO:00511...      NAS  ...   \n",
       "425053                                                 {}      NAS  ...   \n",
       "425054  {GO:0051234, GO:0055085, GO:0006810, BFO:00000...      NAS  ...   \n",
       "425055  {GO:0051234, GO:0006810, BFO:0000015, GO:00511...      NAS  ...   \n",
       "432681  {GO:0032501, GO:0050953, GO:0003008, BFO:00000...      TAS  ...   \n",
       "\n",
       "                   pubs     release pmid_new is_new fresh pmid_removed unique  \\\n",
       "401144  [PMID:26763933]  2024-06-10      NaN    NaN   NaN         True   True   \n",
       "401146  [PMID:26763933]  2024-06-10      NaN    NaN   NaN         True   True   \n",
       "453842  [PMID:31076723]  2024-06-10      NaN    NaN   NaN         True   True   \n",
       "587451  [PMID:28640956]  2024-06-10      NaN    NaN   NaN         True   True   \n",
       "587452  [PMID:28640956]  2024-06-10      NaN    NaN   NaN         True   True   \n",
       "...                 ...         ...      ...    ...   ...          ...    ...   \n",
       "424250  [PMID:10072596]  2020-01-01      NaN    NaN   NaN         True   True   \n",
       "425053  [PMID:10072596]  2020-01-01      NaN    NaN   NaN         True   True   \n",
       "425054  [PMID:10072596]  2020-01-01      NaN    NaN   NaN         True   True   \n",
       "425055  [PMID:10072596]  2020-01-01      NaN    NaN   NaN         True   True   \n",
       "432681  [PMID:10362512]  2020-01-01      NaN    NaN   NaN         True   True   \n",
       "\n",
       "       redacted redundant iba_rejected  \n",
       "401144     True     False        False  \n",
       "401146     True     False        False  \n",
       "453842     True     False        False  \n",
       "587451     True     False        False  \n",
       "587452     True     False        False  \n",
       "...         ...       ...          ...  \n",
       "424250     True     False        False  \n",
       "425053     True     False        False  \n",
       "425054     True     False        False  \n",
       "425055     True     False        False  \n",
       "432681     True     False        False  \n",
       "\n",
       "[83 rows x 23 columns]"
      ],
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>subject</th>\n",
       "      <th>subject_label</th>\n",
       "      <th>predicate</th>\n",
       "      <th>object</th>\n",
       "      <th>object_label</th>\n",
       "      <th>object_obsoletes</th>\n",
       "      <th>object_uninformative</th>\n",
       "      <th>object_closure</th>\n",
       "      <th>object_closure_redundant</th>\n",
       "      <th>evidence</th>\n",
       "      <th>...</th>\n",
       "      <th>pubs</th>\n",
       "      <th>release</th>\n",
       "      <th>pmid_new</th>\n",
       "      <th>is_new</th>\n",
       "      <th>fresh</th>\n",
       "      <th>pmid_removed</th>\n",
       "      <th>unique</th>\n",
       "      <th>redacted</th>\n",
       "      <th>redundant</th>\n",
       "      <th>iba_rejected</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>401144</th>\n",
       "      <td>UniProtKB:Q8N6R0</td>\n",
       "      <td>METTL13</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0000122</td>\n",
       "      <td>negative regulation of transcription by RNA po...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{BFO:0000015, GO:0006357, GO:0008150, GO:00098...</td>\n",
       "      <td>{GO:0045934, GO:0009892, GO:0065007, GO:000988...</td>\n",
       "      <td>IMP</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:26763933]</td>\n",
       "      <td>2024-06-10</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>401146</th>\n",
       "      <td>UniProtKB:Q8N6R0</td>\n",
       "      <td>METTL13</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:1902807</td>\n",
       "      <td>negative regulation of cell cycle G1/S phase t...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0065007, GO:1902806, GO:0010948, GO:190198...</td>\n",
       "      <td>{GO:0065007, GO:0010948, GO:1901988, GO:005172...</td>\n",
       "      <td>IMP</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:26763933]</td>\n",
       "      <td>2024-06-10</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>453842</th>\n",
       "      <td>UniProtKB:Q96K19</td>\n",
       "      <td>RNF170</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0034140</td>\n",
       "      <td>negative regulation of toll-like receptor 3 si...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0048585, GO:0062207, GO:1902532, GO:000996...</td>\n",
       "      <td>{GO:0048585, GO:0065007, GO:0002682, GO:006220...</td>\n",
       "      <td>IDA</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:31076723]</td>\n",
       "      <td>2024-06-10</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>587451</th>\n",
       "      <td>RNAcentral:URS0000083D87_9606</td>\n",
       "      <td>URS0000083D87_9606</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0035195</td>\n",
       "      <td>miRNA-mediated post-transcriptional gene silen...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{BFO:0000015, GO:0016441, GO:0008150, GO:00106...</td>\n",
       "      <td>{GO:0065007, GO:0009892, GO:0031047, GO:000988...</td>\n",
       "      <td>IDA</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:28640956]</td>\n",
       "      <td>2024-06-10</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>587452</th>\n",
       "      <td>RNAcentral:URS0000083D87_9606</td>\n",
       "      <td>URS0000083D87_9606</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0090051</td>\n",
       "      <td>negative regulation of cell migration involved...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0030336, BFO:0000015, GO:0008150, GO:00105...</td>\n",
       "      <td>{GO:0065007, GO:0030336, BFO:0000015, GO:00485...</td>\n",
       "      <td>IGI</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:28640956]</td>\n",
       "      <td>2024-06-10</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>424250</th>\n",
       "      <td>UniProtKB:Q9Y226</td>\n",
       "      <td>SLC22A13</td>\n",
       "      <td>None</td>\n",
       "      <td>GO:0015695</td>\n",
       "      <td>organic cation transport</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0051234, GO:0006810, BFO:0000015, GO:00156...</td>\n",
       "      <td>{GO:0051234, GO:0006810, BFO:0000015, GO:00511...</td>\n",
       "      <td>NAS</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:10072596]</td>\n",
       "      <td>2020-01-01</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>425053</th>\n",
       "      <td>UniProtKB:Q9Y267</td>\n",
       "      <td>SLC22A14</td>\n",
       "      <td>None</td>\n",
       "      <td>GO:0005887</td>\n",
       "      <td>None</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0005887}</td>\n",
       "      <td>{}</td>\n",
       "      <td>NAS</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:10072596]</td>\n",
       "      <td>2020-01-01</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>425054</th>\n",
       "      <td>UniProtKB:Q9Y267</td>\n",
       "      <td>SLC22A14</td>\n",
       "      <td>None</td>\n",
       "      <td>GO:0015101</td>\n",
       "      <td>organic cation transmembrane transporter activity</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0051234, GO:0055085, GO:0006810, BFO:00000...</td>\n",
       "      <td>{GO:0051234, GO:0055085, GO:0006810, BFO:00000...</td>\n",
       "      <td>NAS</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:10072596]</td>\n",
       "      <td>2020-01-01</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>425055</th>\n",
       "      <td>UniProtKB:Q9Y267</td>\n",
       "      <td>SLC22A14</td>\n",
       "      <td>None</td>\n",
       "      <td>GO:0015695</td>\n",
       "      <td>organic cation transport</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0051234, GO:0006810, BFO:0000015, GO:00156...</td>\n",
       "      <td>{GO:0051234, GO:0006810, BFO:0000015, GO:00511...</td>\n",
       "      <td>NAS</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:10072596]</td>\n",
       "      <td>2020-01-01</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>432681</th>\n",
       "      <td>UniProtKB:Q9Y5M6</td>\n",
       "      <td>OCLM</td>\n",
       "      <td>None</td>\n",
       "      <td>GO:0007601</td>\n",
       "      <td>visual perception</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0032501, GO:0050953, GO:0003008, BFO:00000...</td>\n",
       "      <td>{GO:0032501, GO:0050953, GO:0003008, BFO:00000...</td>\n",
       "      <td>TAS</td>\n",
       "      <td>...</td>\n",
       "      <td>[PMID:10362512]</td>\n",
       "      <td>2020-01-01</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>83 rows × 23 columns</p>\n",
       "</div>"
      ]
     },
     "execution_count": 345,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "execution_count": 345
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T04:59:37.662072Z",
     "start_time": "2025-01-06T04:59:37.623828Z"
    }
   },
   "cell_type": "code",
   "source": [
    "cases = [row_to_test_case(row) for _, row in redacted_df.iterrows()]\n",
    "\n",
    "with open(\"output/test-cases-redacted.yaml\", \"w\") as f:\n",
    "    yaml.dump({\"cases\": cases}, f, sort_keys=False)"
   ],
   "id": "5a9d77bbe489741c",
   "outputs": [],
   "execution_count": 346
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T16:24:14.051640Z",
     "start_time": "2025-01-06T16:24:13.956972Z"
    }
   },
   "cell_type": "code",
   "source": [
    "iba_df = new_human[(new_human['is_iba'] == True) & (new_human['object_uninformative'] == False) & (new_human['negated'] != True) & (new_human['redundant'] != True)]\n",
    "iba_df"
   ],
   "id": "d1d74a1ac92d43c7",
   "outputs": [
    {
     "data": {
      "text/plain": [
       "                 subject subject_label     predicate      object  \\\n",
       "718564  UniProtKB:Q06418         TYRO3       enables  GO:0004714   \n",
       "718565  UniProtKB:P78559         MAP1A  is_active_in  GO:0030425   \n",
       "718566  UniProtKB:Q7L1W4        LRRC8D  is_active_in  GO:0005737   \n",
       "718567  UniProtKB:A3QJZ7      PRAMEF27       part_of  GO:0031462   \n",
       "718568  UniProtKB:Q70IA6          MOB2  is_active_in  GO:0005634   \n",
       "...                  ...           ...           ...         ...   \n",
       "782818  UniProtKB:Q9NZC2         TREM2   involved_in  GO:0045088   \n",
       "782819  UniProtKB:Q9Y2K2          SIK3       enables  GO:0050321   \n",
       "782820  UniProtKB:P43235          CTSK   involved_in  GO:0051603   \n",
       "782821  UniProtKB:Q07343         PDE4B       enables  GO:0047555   \n",
       "782822  UniProtKB:A6NC42         DPPA5   involved_in  GO:0010468   \n",
       "\n",
       "                                             object_label  object_obsoletes  \\\n",
       "718564  transmembrane receptor protein tyrosine kinase...             False   \n",
       "718565                                           dendrite             False   \n",
       "718566                                          cytoplasm             False   \n",
       "718567                 Cul2-RING ubiquitin ligase complex             False   \n",
       "718568                                            nucleus             False   \n",
       "...                                                   ...               ...   \n",
       "782818               regulation of innate immune response             False   \n",
       "782819                        tau-protein kinase activity             False   \n",
       "782820  proteolysis involved in protein catabolic process             False   \n",
       "782821        3',5'-cyclic-GMP phosphodiesterase activity             False   \n",
       "782822                      regulation of gene expression             False   \n",
       "\n",
       "        object_uninformative  \\\n",
       "718564                 False   \n",
       "718565                 False   \n",
       "718566                 False   \n",
       "718567                 False   \n",
       "718568                 False   \n",
       "...                      ...   \n",
       "782818                 False   \n",
       "782819                 False   \n",
       "782820                 False   \n",
       "782821                 False   \n",
       "782822                 False   \n",
       "\n",
       "                                           object_closure  \\\n",
       "718564  {GO:0019199, GO:0140096, GO:0003824, GO:001674...   \n",
       "718565  {GO:0030425, GO:0120025, GO:0043005, GO:011016...   \n",
       "718566  {CARO:0030000, UBERON:0000061, CARO:0000003, G...   \n",
       "718567  {GO:0031462, GO:0031461, GO:1990234, BFO:00000...   \n",
       "718568  {GO:0110165, GO:0043231, BFO:0000002, GO:00432...   \n",
       "...                                                   ...   \n",
       "782818  {GO:0065007, GO:0002682, GO:0050776, BFO:00000...   \n",
       "782819  {GO:0140096, GO:0003824, GO:0004674, GO:001674...   \n",
       "782820  {GO:0043170, GO:0006508, GO:0044238, GO:000905...   \n",
       "782821  {GO:0047555, GO:0003824, GO:0008081, BFO:00000...   \n",
       "782822  {GO:0065007, GO:0060255, GO:0009889, BFO:00000...   \n",
       "\n",
       "                                 object_closure_redundant evidence  ...  \\\n",
       "718564  {GO:0019199, GO:0003824, BFO:0000015, GO:00167...      IBA  ...   \n",
       "718565  {CARO:0030000, CL:0002319, CL:0000211, UBERON:...      IBA  ...   \n",
       "718566  {CARO:0030000, UBERON:0000061, CARO:0000003, C...      IBA  ...   \n",
       "718567  {GO:0031461, GO:1990234, BFO:0000004, GO:01405...      IBA  ...   \n",
       "718568  {CARO:0030000, CARO:0000000, BFO:0000004, GO:0...      IBA  ...   \n",
       "...                                                   ...      ...  ...   \n",
       "782818  {GO:0065007, GO:0002682, GO:0050776, BFO:00000...      IBA  ...   \n",
       "782819  {GO:0140096, GO:0003824, GO:0004674, GO:001674...      IBA  ...   \n",
       "782820  {GO:0043170, GO:0006508, GO:0044238, GO:000905...      IBA  ...   \n",
       "782821  {GO:0003824, GO:0008081, BFO:0000015, GO:00425...      IBA  ...   \n",
       "782822  {GO:0065007, GO:0060255, GO:0009889, BFO:00000...      IBA  ...   \n",
       "\n",
       "                    pubs     release pmid_new is_new  fresh pmid_removed  \\\n",
       "718564  [GO_REF:0000033]  2024-11-03    False  False  False          NaN   \n",
       "718565  [GO_REF:0000033]  2024-11-03    False  False  False          NaN   \n",
       "718566  [GO_REF:0000033]  2024-11-03    False  False  False          NaN   \n",
       "718567  [GO_REF:0000033]  2024-11-03    False   True  False          NaN   \n",
       "718568  [GO_REF:0000033]  2024-11-03    False  False  False          NaN   \n",
       "...                  ...         ...      ...    ...    ...          ...   \n",
       "782818  [GO_REF:0000033]  2024-11-03    False  False  False          NaN   \n",
       "782819  [GO_REF:0000033]  2024-11-03    False  False  False          NaN   \n",
       "782820  [GO_REF:0000033]  2024-11-03    False  False  False          NaN   \n",
       "782821  [GO_REF:0000033]  2024-11-03    False  False  False          NaN   \n",
       "782822  [GO_REF:0000033]  2024-11-03    False  False  False          NaN   \n",
       "\n",
       "       unique redacted redundant iba_rejected  \n",
       "718564    NaN      NaN     False        False  \n",
       "718565    NaN      NaN     False        False  \n",
       "718566    NaN      NaN     False        False  \n",
       "718567    NaN      NaN     False        False  \n",
       "718568    NaN      NaN     False        False  \n",
       "...       ...      ...       ...          ...  \n",
       "782818    NaN      NaN     False        False  \n",
       "782819    NaN      NaN     False        False  \n",
       "782820    NaN      NaN     False        False  \n",
       "782821    NaN      NaN     False        False  \n",
       "782822    NaN      NaN     False        False  \n",
       "\n",
       "[56487 rows x 23 columns]"
      ],
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>subject</th>\n",
       "      <th>subject_label</th>\n",
       "      <th>predicate</th>\n",
       "      <th>object</th>\n",
       "      <th>object_label</th>\n",
       "      <th>object_obsoletes</th>\n",
       "      <th>object_uninformative</th>\n",
       "      <th>object_closure</th>\n",
       "      <th>object_closure_redundant</th>\n",
       "      <th>evidence</th>\n",
       "      <th>...</th>\n",
       "      <th>pubs</th>\n",
       "      <th>release</th>\n",
       "      <th>pmid_new</th>\n",
       "      <th>is_new</th>\n",
       "      <th>fresh</th>\n",
       "      <th>pmid_removed</th>\n",
       "      <th>unique</th>\n",
       "      <th>redacted</th>\n",
       "      <th>redundant</th>\n",
       "      <th>iba_rejected</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>718564</th>\n",
       "      <td>UniProtKB:Q06418</td>\n",
       "      <td>TYRO3</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:0004714</td>\n",
       "      <td>transmembrane receptor protein tyrosine kinase...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0019199, GO:0140096, GO:0003824, GO:001674...</td>\n",
       "      <td>{GO:0019199, GO:0003824, BFO:0000015, GO:00167...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>...</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>718565</th>\n",
       "      <td>UniProtKB:P78559</td>\n",
       "      <td>MAP1A</td>\n",
       "      <td>is_active_in</td>\n",
       "      <td>GO:0030425</td>\n",
       "      <td>dendrite</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0030425, GO:0120025, GO:0043005, GO:011016...</td>\n",
       "      <td>{CARO:0030000, CL:0002319, CL:0000211, UBERON:...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>...</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>718566</th>\n",
       "      <td>UniProtKB:Q7L1W4</td>\n",
       "      <td>LRRC8D</td>\n",
       "      <td>is_active_in</td>\n",
       "      <td>GO:0005737</td>\n",
       "      <td>cytoplasm</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{CARO:0030000, UBERON:0000061, CARO:0000003, G...</td>\n",
       "      <td>{CARO:0030000, UBERON:0000061, CARO:0000003, C...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>...</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>718567</th>\n",
       "      <td>UniProtKB:A3QJZ7</td>\n",
       "      <td>PRAMEF27</td>\n",
       "      <td>part_of</td>\n",
       "      <td>GO:0031462</td>\n",
       "      <td>Cul2-RING ubiquitin ligase complex</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0031462, GO:0031461, GO:1990234, BFO:00000...</td>\n",
       "      <td>{GO:0031461, GO:1990234, BFO:0000004, GO:01405...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>...</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>718568</th>\n",
       "      <td>UniProtKB:Q70IA6</td>\n",
       "      <td>MOB2</td>\n",
       "      <td>is_active_in</td>\n",
       "      <td>GO:0005634</td>\n",
       "      <td>nucleus</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0110165, GO:0043231, BFO:0000002, GO:00432...</td>\n",
       "      <td>{CARO:0030000, CARO:0000000, BFO:0000004, GO:0...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>...</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>782818</th>\n",
       "      <td>UniProtKB:Q9NZC2</td>\n",
       "      <td>TREM2</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0045088</td>\n",
       "      <td>regulation of innate immune response</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0065007, GO:0002682, GO:0050776, BFO:00000...</td>\n",
       "      <td>{GO:0065007, GO:0002682, GO:0050776, BFO:00000...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>...</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>782819</th>\n",
       "      <td>UniProtKB:Q9Y2K2</td>\n",
       "      <td>SIK3</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:0050321</td>\n",
       "      <td>tau-protein kinase activity</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0140096, GO:0003824, GO:0004674, GO:001674...</td>\n",
       "      <td>{GO:0140096, GO:0003824, GO:0004674, GO:001674...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>...</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>782820</th>\n",
       "      <td>UniProtKB:P43235</td>\n",
       "      <td>CTSK</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0051603</td>\n",
       "      <td>proteolysis involved in protein catabolic process</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0043170, GO:0006508, GO:0044238, GO:000905...</td>\n",
       "      <td>{GO:0043170, GO:0006508, GO:0044238, GO:000905...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>...</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>782821</th>\n",
       "      <td>UniProtKB:Q07343</td>\n",
       "      <td>PDE4B</td>\n",
       "      <td>enables</td>\n",
       "      <td>GO:0047555</td>\n",
       "      <td>3',5'-cyclic-GMP phosphodiesterase activity</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0047555, GO:0003824, GO:0008081, BFO:00000...</td>\n",
       "      <td>{GO:0003824, GO:0008081, BFO:0000015, GO:00425...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>...</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>782822</th>\n",
       "      <td>UniProtKB:A6NC42</td>\n",
       "      <td>DPPA5</td>\n",
       "      <td>involved_in</td>\n",
       "      <td>GO:0010468</td>\n",
       "      <td>regulation of gene expression</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>{GO:0065007, GO:0060255, GO:0009889, BFO:00000...</td>\n",
       "      <td>{GO:0065007, GO:0060255, GO:0009889, BFO:00000...</td>\n",
       "      <td>IBA</td>\n",
       "      <td>...</td>\n",
       "      <td>[GO_REF:0000033]</td>\n",
       "      <td>2024-11-03</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>56487 rows × 23 columns</p>\n",
       "</div>"
      ]
     },
     "execution_count": 348,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "execution_count": 348
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-01-06T16:39:47.734345Z",
     "start_time": "2025-01-06T16:39:44.937046Z"
    }
   },
   "cell_type": "code",
   "source": [
    "with open(\"output/test-cases-iba.yaml\", \"w\") as f:\n",
    "    yaml.dump({\"cases\": df_to_test_cases(iba_df, limit=1000)}, f, sort_keys=False)"
   ],
   "id": "8cd8667bbc5568c0",
   "outputs": [],
   "execution_count": 351
  },
  {
   "metadata": {},
   "cell_type": "code",
   "outputs": [],
   "execution_count": null,
   "source": "",
   "id": "47d31b2f387a2dc0"
  }
 ],
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