{ "cells": [ { "cell_type": "markdown", "id": "78b91fea", "metadata": {}, "source": [ "# Exploration of MAxO\n", "\n", "The Medical Action Ontology (MAxO) (https://obofoundry.org/ontology/maxo) is an ontology of medical procedures, interventions, therapies, and treatments for disease with an emphasis on rare disease (RD).\n", "\n", "This notebooks shows an exploration of the contents of MAxO. It focuses on the ontology content, but as\n", "annotations are added we will include these." ] }, { "cell_type": "markdown", "id": "04c53044", "metadata": {}, "source": [ "## Setup\n", "\n", "We will use the sqlite version of MAxO. In this notebook we will set up an alias for convenience.\n", "\n", "Note on the command line the syntax is different, for unix systems:\n", "\n", "```bash\n", "alias maxo=\"runoak -i sqlite:obo:maxo\"\n", "```" ] }, { "cell_type": "code", "execution_count": 21, "id": "c842d3e5", "metadata": {}, "outputs": [], "source": [ "%alias maxo runoak -i sqlite:obo:maxo" ] }, { "cell_type": "markdown", "id": "5e8fc4b2", "metadata": {}, "source": [ "Let's start by getting some basic metadata about the ontology.\n", "\n", "__NOTE__ the first time you run this there may be a lag while the pre-made sqlite database for maxo is downloaded" ] }, { "cell_type": "code", "execution_count": 4, "id": "679b70d6", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "dce:creator:\r\n", "- Leigh Carmody\r\n", "- Peter Robinson\r\n", "dce:description:\r\n", "- An ontology to represent medically relevant actions, procedures, therapies, interventions,\r\n", " and recommendations.\r\n", "dce:title:\r\n", "- Medical Action Ontology\r\n", "dcterms:license:\r\n", "- \r\n", "id:\r\n", "- obo:maxo.owl\r\n", "owl:versionIRI:\r\n", "- obo:maxo/releases/2022-12-19/maxo.owl\r\n", "owl:versionInfo:\r\n", "- '2022-12-19'\r\n", "rdf:type:\r\n", "- owl:Ontology\r\n", "rdfs:isDefinedBy:\r\n", "- http://purl.obolibrary.org/obo/obo.owl\r\n", "schema:url:\r\n", "- http://purl.obolibrary.org/obo/maxo.owl\r\n", "sh:prefix:\r\n", "- obo\r\n" ] } ], "source": [ "maxo ontology-metadata --all" ] }, { "cell_type": "markdown", "id": "b17efc3a", "metadata": {}, "source": [ "## Root terms\n", "\n", "We will query for roots (all terms without an is-a parent)\n", "\n", "This reveals a few dangling classes that should be cleared up" ] }, { "cell_type": "code", "execution_count": 5, "id": "26f6b28d", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "id\tlabel\n", "BFO:0000001\tentity\n", "CARO:0000003\tNone\n", "CARO:0000006\tNone\n", "CARO:0001001\tNone\n", "CARO:0001010\tNone\n", "CARO:0010000\tNone\n", "CL:0000000\tcell\n", "CL:0017500\tneutrophillic cytoplasm\n", "CL:0017502\tacidophilic cytoplasm\n", "CL:0017503\tbasophilic cytoplasm\n", "CL:0017504\tpolychromatophilic cytoplasm\n", "CL:0017505\tincreased nucleus size\n", "HP:0000001\tAll\n", "MAXO:0000001\tmedical action\n", "NCBITaxon:110815\tNone\n", "NCBITaxon:147099\tNone\n", "NCBITaxon:147554\tNone\n", "NCBITaxon:189497\tNone\n", "NCBITaxon:3176\tNone\n", "NCBITaxon:3312\tNone\n", "NCBITaxon:33630\tNone\n", "NCBITaxon:33682\tNone\n", "NCBITaxon:3378\tNone\n", "NCBITaxon:38254\tNone\n", "NCBITaxon:4891\tNone\n", "NCBITaxon:4895\tNone\n", "NCBITaxon:4896\tNone\n", "NCBITaxon:4932\tNone\n", "NCBITaxon:5782\tNone\n", "NCBITaxon:Union_0000023\tNone\n", "SO:0000110\tsequence_feature\n" ] } ], "source": [ "maxo roots -p i" ] }, { "cell_type": "markdown", "id": "1e2c9939", "metadata": {}, "source": [ "### Roots in the MAXO id space\n", "\n", "As can be seen above there is a single root node in the MAXO namespace\n", "\n", "We can also query for MAXO-roots, i.e classes in MAXO that have no MAXO is-a parent:" ] }, { "cell_type": "code", "execution_count": 7, "id": "58767b49", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "id\tlabel\r", "\r\n", "MAXO:0000001\tmedical action\r", "\r\n" ] } ], "source": [ "maxo roots -p i --has-prefix MAXO" ] }, { "cell_type": "markdown", "id": "0ad599d8", "metadata": {}, "source": [ "## Visualization\n", "\n", "\n", "We can use the `viz` command to see the full ancestry for any term or set of terms or term query.\n", "\n", "For now, we will restrict to is-a parents (`-p i`):" ] }, { "cell_type": "code", "execution_count": 5, "id": "56f70a02", "metadata": {}, "outputs": [], "source": [ "maxo viz -p i 'biopsy of thymus' 'biopsy of thyroid gland' -o output/maxo-biopsy.png" ] }, { "cell_type": "markdown", "id": "19033a67", "metadata": {}, "source": [ "![img](output/maxo-biopsy.png)" ] }, { "cell_type": "markdown", "id": "b98a19e7", "metadata": {}, "source": [ "__TODO__: add explanation of why BFO processes show up" ] }, { "cell_type": "markdown", "id": "445ca573", "metadata": {}, "source": [ "## Upper level\n", "\n", "We can use the `tree` command to explore the upper level:\n", "\n" ] }, { "cell_type": "code", "execution_count": 8, "id": "88df2715", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "* [] **MAXO:0000001 ! medical action**\r\n", " * [i] **MAXO:0000002 ! therapeutic procedure**\r\n", " * [i] **MAXO:0000058 ! pharmacotherapy**\r\n", " * [i] **MAXO:0000003 ! diagnostic procedure**\r\n", " * [i] **MAXO:0000013 ! complementary and alternative medical therapy**\r\n", " * [i] **MAXO:0000017 ! preventative therapeutics**\r\n", " * [i] **MAXO:0000021 ! palliative care**\r\n", " * [i] **MAXO:0001014 ! medical action avoidance**\r\n" ] } ], "source": [ "maxo tree -p i MAXO:0000001 MAXO:0000058 MAXO:0000002 MAXO:0000003 MAXO:0000013 MAXO:0000017 MAXO:0000021 MAXO:0001014" ] }, { "cell_type": "markdown", "id": "343bb386", "metadata": {}, "source": [ "## Summary Statistics\n", "\n", "We can get summary statistics using the `statistics` command.\n", "\n", "Note that like many ontologies, MAXO comes \"bundled\" with other ontologies, so it's important to pass in\n", "`--has-prefix` to restrict summary statistics only to things in the MAXO space.\n" ] }, { "cell_type": "code", "execution_count": 22, "id": "0d906ccf", "metadata": {}, "outputs": [], "source": [ "maxo statistics --has-prefix MAXO > output/maxo-stats.yaml" ] }, { "cell_type": "markdown", "id": "6b5a48ce", "metadata": {}, "source": [ "This generates a YAML object (download from [output/maxo-stats.yaml](output/maxo-stats.yaml)).\n", "\n", "let's take a look at the output. It's quite large so we'll use the unix `head` command:" ] }, { "cell_type": "code", "execution_count": 23, "id": "f6ace34c", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "annotation_property_count: 0\r\n", "class_count: 1440\r\n", "class_count_with_text_definitions: 1374\r\n", "class_count_without_text_definitions: 66\r\n", "contributor_summary:\r\n", " :\r\n", " contributor_id: \r\n", " role_counts:\r\n", " oio:created_by:\r\n", " facet: oio:created_by\r\n", " filtered_count: 822\r\n", " :\r\n", " contributor_id: \r\n", " role_counts:\r\n", " oio:created_by:\r\n", " facet: oio:created_by\r\n", " filtered_count: 3\r\n", " http://orcid.org/0000-0001-7941-2961:\r\n", " contributor_id: http://orcid.org/0000-0001-7941-2961\r\n", " contributor_name: http://orcid.org/0000-0001-7941-2961\r\n", " role_counts:\r\n", " oio:created_by:\r\n", " facet: oio:created_by\r\n", " filtered_count: 491\r\n", " http://orcid.org/0000-0001-7941-29610:\r\n" ] } ], "source": [ "!head -25 output/maxo-stats.yaml" ] }, { "cell_type": "markdown", "id": "8aa5eb9d", "metadata": {}, "source": [ "Note that the main stats are buried further down.\n" ] }, { "cell_type": "markdown", "id": "f198d551", "metadata": {}, "source": [ "You can get the same thing in JSON. There is a cached copy you can view on https://jsonblob.com/1069350711447535616" ] }, { "cell_type": "code", "execution_count": 24, "id": "358f5b52", "metadata": {}, "outputs": [], "source": [ "maxo statistics --has-prefix MAXO -O json > output/maxo-stats.json" ] }, { "cell_type": "markdown", "id": "51b33ffe", "metadata": {}, "source": [ "The YAML and JSON view is best for seeing the more complete granular results, but for many purposes a tabular view is better.\n", "\n", "We can do that with `-O csv` (the `-O` is short for `--output-type`, which is available\n", "for more OAK commands)" ] }, { "cell_type": "code", "execution_count": 25, "id": "f7227a84", "metadata": {}, "outputs": [], "source": [ "maxo statistics --has-prefix MAXO -O csv -o output/maxo-stats.tsv" ] }, { "cell_type": "markdown", "id": "3072c21d", "metadata": {}, "source": [ "Download: [output/maxo-stats.tsv](output/maxo-stats.tsv)\n", "\n", "You can then browse the output using whatever method you prefer, e.g. load into excel.\n", "\n", "In a Jupyter notebook, pandas dataframes are a convenient way to explore tabular data:" ] }, { "cell_type": "code", "execution_count": 32, "id": "60afb3b9", "metadata": {}, "outputs": [], "source": [ "import pandas as pd\n", "pd.set_option('display.max_columns', None)\n", "pd.set_option('display.max_rows', None)" ] }, { "cell_type": "code", "execution_count": 33, "id": "7cb6bb7e", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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idcompared_withagentsclass_countdeprecated_class_countnon_deprecated_class_countclass_count_with_text_definitionsclass_count_without_text_definitionsobject_property_countannotation_property_countnamed_individual_countsubset_countrdf_triple_countsubclass_of_axiom_countequivalent_classes_axiom_countentailed_edge_count_by_predicatedistinct_synonym_countsynonym_statement_countclass_count_by_categorycontributor_summarychange_summarymerged_class_querydeprecated_property_countedge_count_by_predicate_BFO:0000051edge_count_by_predicate_MAXO:0000521edge_count_by_predicate_MAXO:0000864edge_count_by_predicate_MAXO:0001015edge_count_by_predicate_MAXO:0001027edge_count_by_predicate_RO:0002233edge_count_by_predicate_rdfs:subClassOfsynonym_statement_count_by_predicate_hasBroadSynonymsynonym_statement_count_by_predicate_hasExactSynonymsynonym_statement_count_by_predicate_hasNarrowSynonymsynonym_statement_count_by_predicate_hasRelatedSynonymmapping_statement_count_by_predicate_hasDbXrefmapping_statement_count_by_object_source_OGMSmapping_statement_count_by_object_source_NCITmapping_statement_count_by_object_source_OAEmapping_statement_count_by_object_source_SIOmapping_statement_count_by_object_source_EROmapping_statement_count_by_object_source_NCROmapping_statement_count_by_object_source_SCDOmapping_statement_count_by_object_source_OMITmapping_statement_count_by_object_source_CHEBImapping_statement_count_by_object_source_MeSHmapping_statement_count_by_object_source_OBImapping_statement_count_by_object_source_IDOmapping_statement_count_by_object_source_VOmapping_statement_count_by_object_source_httpsmapping_statement_count_by_object_source_PMIDmapping_statement_count_by_object_source_NCItmapping_statement_count_by_object_source_UMLS_CUImapping_statement_count_by_object_source_CMOmapping_statement_count_by_object_source_NCBIBookmapping_statement_count_by_object_source_MMOmapping_statement_count_by_object_source_VSOmapping_statement_count_by_object_source_httpmapping_statement_count_by_object_source_EFOmapping_statement_count_by_object_source_IDOMALmapping_statement_count_subject_by_object_source_OGMSmapping_statement_count_subject_by_object_source_NCITmapping_statement_count_subject_by_object_source_OAEmapping_statement_count_subject_by_object_source_SIOmapping_statement_count_subject_by_object_source_EROmapping_statement_count_subject_by_object_source_NCROmapping_statement_count_subject_by_object_source_SCDOmapping_statement_count_subject_by_object_source_OMITmapping_statement_count_subject_by_object_source_CHEBImapping_statement_count_subject_by_object_source_MeSHmapping_statement_count_subject_by_object_source_OBImapping_statement_count_subject_by_object_source_IDOmapping_statement_count_subject_by_object_source_VOmapping_statement_count_subject_by_object_source_httpsmapping_statement_count_subject_by_object_source_PMIDmapping_statement_count_subject_by_object_source_NCItmapping_statement_count_subject_by_object_source_UMLS_CUImapping_statement_count_subject_by_object_source_CMOmapping_statement_count_subject_by_object_source_NCBIBookmapping_statement_count_subject_by_object_source_MMOmapping_statement_count_subject_by_object_source_VSOmapping_statement_count_subject_by_object_source_httpmapping_statement_count_subject_by_object_source_EFOmapping_statement_count_subject_by_object_source_IDOMALwas_generated_by_started_at_timewas_generated_by_was_associated_withwas_generated_by_acted_on_behalf_ofontologies_idontologies_versionontologies_version_info
0AllOntologies[][]14405313871374664000156422842584{}43914391{}{'http://orcid.org/0000-0001-7941-2961': Contr...{}0082013497644121542542509719554833021425513420151431111651421183212142551332015143111165142112023-01-29T12:44:00.348450OAKcjmobo:maxo.owlobo:maxo/releases/2022-12-19/maxo.owl2022-12-19
\n", "
" ], "text/plain": [ " id compared_with agents class_count deprecated_class_count \\\n", "0 AllOntologies [] [] 1440 53 \n", "\n", " non_deprecated_class_count class_count_with_text_definitions \\\n", "0 1387 1374 \n", "\n", " class_count_without_text_definitions object_property_count \\\n", "0 66 4 \n", "\n", " annotation_property_count named_individual_count subset_count \\\n", "0 0 0 0 \n", "\n", " rdf_triple_count subclass_of_axiom_count equivalent_classes_axiom_count \\\n", "0 15642 2842 584 \n", "\n", " entailed_edge_count_by_predicate distinct_synonym_count \\\n", "0 {} 4391 \n", "\n", " synonym_statement_count class_count_by_category \\\n", "0 4391 {} \n", "\n", " contributor_summary change_summary \\\n", "0 {'http://orcid.org/0000-0001-7941-2961': Contr... {} \n", "\n", " merged_class_query deprecated_property_count \\\n", "0 0 0 \n", "\n", " edge_count_by_predicate_BFO:0000051 edge_count_by_predicate_MAXO:0000521 \\\n", "0 8 20 \n", "\n", " edge_count_by_predicate_MAXO:0000864 edge_count_by_predicate_MAXO:0001015 \\\n", "0 134 9 \n", "\n", " edge_count_by_predicate_MAXO:0001027 edge_count_by_predicate_RO:0002233 \\\n", "0 76 441 \n", "\n", " edge_count_by_predicate_rdfs:subClassOf \\\n", "0 2154 \n", "\n", " synonym_statement_count_by_predicate_hasBroadSynonym \\\n", "0 25 \n", "\n", " synonym_statement_count_by_predicate_hasExactSynonym \\\n", "0 4250 \n", "\n", " synonym_statement_count_by_predicate_hasNarrowSynonym \\\n", "0 97 \n", "\n", " synonym_statement_count_by_predicate_hasRelatedSynonym \\\n", "0 19 \n", "\n", " mapping_statement_count_by_predicate_hasDbXref \\\n", "0 554 \n", "\n", " mapping_statement_count_by_object_source_OGMS \\\n", "0 8 \n", "\n", " mapping_statement_count_by_object_source_NCIT \\\n", "0 330 \n", "\n", " mapping_statement_count_by_object_source_OAE \\\n", "0 2 \n", "\n", " mapping_statement_count_by_object_source_SIO \\\n", "0 1 \n", "\n", " mapping_statement_count_by_object_source_ERO \\\n", "0 4 \n", "\n", " mapping_statement_count_by_object_source_NCRO \\\n", "0 2 \n", "\n", " mapping_statement_count_by_object_source_SCDO \\\n", "0 5 \n", "\n", " mapping_statement_count_by_object_source_OMIT \\\n", "0 5 \n", "\n", " mapping_statement_count_by_object_source_CHEBI \\\n", "0 134 \n", "\n", " mapping_statement_count_by_object_source_MeSH \\\n", "0 20 \n", "\n", " mapping_statement_count_by_object_source_OBI \\\n", "0 15 \n", "\n", " mapping_statement_count_by_object_source_IDO \\\n", "0 1 \n", "\n", " mapping_statement_count_by_object_source_VO \\\n", "0 4 \n", "\n", " mapping_statement_count_by_object_source_https \\\n", "0 3 \n", "\n", " mapping_statement_count_by_object_source_PMID \\\n", "0 11 \n", "\n", " mapping_statement_count_by_object_source_NCIt \\\n", "0 1 \n", "\n", " mapping_statement_count_by_object_source_UMLS_CUI \\\n", "0 1 \n", "\n", " mapping_statement_count_by_object_source_CMO \\\n", "0 6 \n", "\n", " mapping_statement_count_by_object_source_NCBIBook \\\n", "0 5 \n", "\n", " mapping_statement_count_by_object_source_MMO \\\n", "0 1 \n", "\n", " mapping_statement_count_by_object_source_VSO \\\n", "0 4 \n", "\n", " mapping_statement_count_by_object_source_http \\\n", "0 2 \n", "\n", " mapping_statement_count_by_object_source_EFO \\\n", "0 1 \n", "\n", " mapping_statement_count_by_object_source_IDOMAL \\\n", "0 1 \n", "\n", " mapping_statement_count_subject_by_object_source_OGMS \\\n", "0 8 \n", "\n", " mapping_statement_count_subject_by_object_source_NCIT \\\n", "0 321 \n", "\n", " mapping_statement_count_subject_by_object_source_OAE \\\n", "0 2 \n", "\n", " mapping_statement_count_subject_by_object_source_SIO \\\n", "0 1 \n", "\n", " mapping_statement_count_subject_by_object_source_ERO \\\n", "0 4 \n", "\n", " mapping_statement_count_subject_by_object_source_NCRO \\\n", "0 2 \n", "\n", " mapping_statement_count_subject_by_object_source_SCDO \\\n", "0 5 \n", "\n", " mapping_statement_count_subject_by_object_source_OMIT \\\n", "0 5 \n", "\n", " mapping_statement_count_subject_by_object_source_CHEBI \\\n", "0 133 \n", "\n", " mapping_statement_count_subject_by_object_source_MeSH \\\n", "0 20 \n", "\n", " mapping_statement_count_subject_by_object_source_OBI \\\n", "0 15 \n", "\n", " mapping_statement_count_subject_by_object_source_IDO \\\n", "0 1 \n", "\n", " mapping_statement_count_subject_by_object_source_VO \\\n", "0 4 \n", "\n", " mapping_statement_count_subject_by_object_source_https \\\n", "0 3 \n", "\n", " mapping_statement_count_subject_by_object_source_PMID \\\n", "0 11 \n", "\n", " mapping_statement_count_subject_by_object_source_NCIt \\\n", "0 1 \n", "\n", " mapping_statement_count_subject_by_object_source_UMLS_CUI \\\n", "0 1 \n", "\n", " mapping_statement_count_subject_by_object_source_CMO \\\n", "0 6 \n", "\n", " mapping_statement_count_subject_by_object_source_NCBIBook \\\n", "0 5 \n", "\n", " mapping_statement_count_subject_by_object_source_MMO \\\n", "0 1 \n", "\n", " mapping_statement_count_subject_by_object_source_VSO \\\n", "0 4 \n", "\n", " mapping_statement_count_subject_by_object_source_http \\\n", "0 2 \n", "\n", " mapping_statement_count_subject_by_object_source_EFO \\\n", "0 1 \n", "\n", " mapping_statement_count_subject_by_object_source_IDOMAL \\\n", "0 1 \n", "\n", " was_generated_by_started_at_time was_generated_by_was_associated_with \\\n", "0 2023-01-29T12:44:00.348450 OAK \n", "\n", " was_generated_by_acted_on_behalf_of ontologies_id \\\n", "0 cjm obo:maxo.owl \n", "\n", " ontologies_version ontologies_version_info \n", "0 obo:maxo/releases/2022-12-19/maxo.owl 2022-12-19 " ] }, "execution_count": 33, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df = pd.read_csv(\"output/maxo-stats.tsv\", sep=\"\\t\").fillna(\"\")\n", "df" ] }, { "cell_type": "markdown", "id": "1693a2d3", "metadata": {}, "source": [ "the default TSV output for most OAK commands follows a TidyData format, with one row per item.\n", "\n", "Let's unpivot this for easy viewing, using pandas `melt`:" ] }, { "cell_type": "code", "execution_count": 34, "id": "aff72a57", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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variablevalue
0idAllOntologies
1compared_with[]
2agents[]
3class_count1440
4deprecated_class_count53
5non_deprecated_class_count1387
6class_count_with_text_definitions1374
7class_count_without_text_definitions66
8object_property_count4
9annotation_property_count0
10named_individual_count0
11subset_count0
12rdf_triple_count15642
13subclass_of_axiom_count2842
14equivalent_classes_axiom_count584
15entailed_edge_count_by_predicate{}
16distinct_synonym_count4391
17synonym_statement_count4391
18class_count_by_category{}
19contributor_summary{'http://orcid.org/0000-0001-7941-2961': Contr...
20change_summary{}
21merged_class_query0
22deprecated_property_count0
23edge_count_by_predicate_BFO:00000518
24edge_count_by_predicate_MAXO:000052120
25edge_count_by_predicate_MAXO:0000864134
26edge_count_by_predicate_MAXO:00010159
27edge_count_by_predicate_MAXO:000102776
28edge_count_by_predicate_RO:0002233441
29edge_count_by_predicate_rdfs:subClassOf2154
30synonym_statement_count_by_predicate_hasBroadS...25
31synonym_statement_count_by_predicate_hasExactS...4250
32synonym_statement_count_by_predicate_hasNarrow...97
33synonym_statement_count_by_predicate_hasRelate...19
34mapping_statement_count_by_predicate_hasDbXref554
35mapping_statement_count_by_object_source_OGMS8
36mapping_statement_count_by_object_source_NCIT330
37mapping_statement_count_by_object_source_OAE2
38mapping_statement_count_by_object_source_SIO1
39mapping_statement_count_by_object_source_ERO4
40mapping_statement_count_by_object_source_NCRO2
41mapping_statement_count_by_object_source_SCDO5
42mapping_statement_count_by_object_source_OMIT5
43mapping_statement_count_by_object_source_CHEBI134
44mapping_statement_count_by_object_source_MeSH20
45mapping_statement_count_by_object_source_OBI15
46mapping_statement_count_by_object_source_IDO1
47mapping_statement_count_by_object_source_VO4
48mapping_statement_count_by_object_source_https3
49mapping_statement_count_by_object_source_PMID11
50mapping_statement_count_by_object_source_NCIt1
51mapping_statement_count_by_object_source_UMLS_CUI1
52mapping_statement_count_by_object_source_CMO6
53mapping_statement_count_by_object_source_NCBIBook5
54mapping_statement_count_by_object_source_MMO1
55mapping_statement_count_by_object_source_VSO4
56mapping_statement_count_by_object_source_http2
57mapping_statement_count_by_object_source_EFO1
58mapping_statement_count_by_object_source_IDOMAL1
59mapping_statement_count_subject_by_object_sour...8
60mapping_statement_count_subject_by_object_sour...321
61mapping_statement_count_subject_by_object_sour...2
62mapping_statement_count_subject_by_object_sour...1
63mapping_statement_count_subject_by_object_sour...4
64mapping_statement_count_subject_by_object_sour...2
65mapping_statement_count_subject_by_object_sour...5
66mapping_statement_count_subject_by_object_sour...5
67mapping_statement_count_subject_by_object_sour...133
68mapping_statement_count_subject_by_object_sour...20
69mapping_statement_count_subject_by_object_sour...15
70mapping_statement_count_subject_by_object_sour...1
71mapping_statement_count_subject_by_object_sour...4
72mapping_statement_count_subject_by_object_sour...3
73mapping_statement_count_subject_by_object_sour...11
74mapping_statement_count_subject_by_object_sour...1
75mapping_statement_count_subject_by_object_sour...1
76mapping_statement_count_subject_by_object_sour...6
77mapping_statement_count_subject_by_object_sour...5
78mapping_statement_count_subject_by_object_sour...1
79mapping_statement_count_subject_by_object_sour...4
80mapping_statement_count_subject_by_object_sour...2
81mapping_statement_count_subject_by_object_sour...1
82mapping_statement_count_subject_by_object_sour...1
83was_generated_by_started_at_time2023-01-29T12:44:00.348450
84was_generated_by_was_associated_withOAK
85was_generated_by_acted_on_behalf_ofcjm
86ontologies_idobo:maxo.owl
87ontologies_versionobo:maxo/releases/2022-12-19/maxo.owl
88ontologies_version_info2022-12-19
\n", "
" ], "text/plain": [ " variable \\\n", "0 id \n", "1 compared_with \n", "2 agents \n", "3 class_count \n", "4 deprecated_class_count \n", "5 non_deprecated_class_count \n", "6 class_count_with_text_definitions \n", "7 class_count_without_text_definitions \n", "8 object_property_count \n", "9 annotation_property_count \n", "10 named_individual_count \n", "11 subset_count \n", "12 rdf_triple_count \n", "13 subclass_of_axiom_count \n", "14 equivalent_classes_axiom_count \n", "15 entailed_edge_count_by_predicate \n", "16 distinct_synonym_count \n", "17 synonym_statement_count \n", "18 class_count_by_category \n", "19 contributor_summary \n", "20 change_summary \n", "21 merged_class_query \n", "22 deprecated_property_count \n", "23 edge_count_by_predicate_BFO:0000051 \n", "24 edge_count_by_predicate_MAXO:0000521 \n", "25 edge_count_by_predicate_MAXO:0000864 \n", "26 edge_count_by_predicate_MAXO:0001015 \n", "27 edge_count_by_predicate_MAXO:0001027 \n", "28 edge_count_by_predicate_RO:0002233 \n", "29 edge_count_by_predicate_rdfs:subClassOf \n", "30 synonym_statement_count_by_predicate_hasBroadS... \n", "31 synonym_statement_count_by_predicate_hasExactS... \n", "32 synonym_statement_count_by_predicate_hasNarrow... \n", "33 synonym_statement_count_by_predicate_hasRelate... \n", "34 mapping_statement_count_by_predicate_hasDbXref \n", "35 mapping_statement_count_by_object_source_OGMS \n", "36 mapping_statement_count_by_object_source_NCIT \n", "37 mapping_statement_count_by_object_source_OAE \n", "38 mapping_statement_count_by_object_source_SIO \n", "39 mapping_statement_count_by_object_source_ERO \n", "40 mapping_statement_count_by_object_source_NCRO \n", "41 mapping_statement_count_by_object_source_SCDO \n", "42 mapping_statement_count_by_object_source_OMIT \n", "43 mapping_statement_count_by_object_source_CHEBI \n", "44 mapping_statement_count_by_object_source_MeSH \n", "45 mapping_statement_count_by_object_source_OBI \n", "46 mapping_statement_count_by_object_source_IDO \n", "47 mapping_statement_count_by_object_source_VO \n", "48 mapping_statement_count_by_object_source_https \n", "49 mapping_statement_count_by_object_source_PMID \n", "50 mapping_statement_count_by_object_source_NCIt \n", "51 mapping_statement_count_by_object_source_UMLS_CUI \n", "52 mapping_statement_count_by_object_source_CMO \n", "53 mapping_statement_count_by_object_source_NCBIBook \n", "54 mapping_statement_count_by_object_source_MMO \n", "55 mapping_statement_count_by_object_source_VSO \n", "56 mapping_statement_count_by_object_source_http \n", "57 mapping_statement_count_by_object_source_EFO \n", "58 mapping_statement_count_by_object_source_IDOMAL \n", "59 mapping_statement_count_subject_by_object_sour... \n", "60 mapping_statement_count_subject_by_object_sour... \n", "61 mapping_statement_count_subject_by_object_sour... \n", "62 mapping_statement_count_subject_by_object_sour... \n", "63 mapping_statement_count_subject_by_object_sour... \n", "64 mapping_statement_count_subject_by_object_sour... \n", "65 mapping_statement_count_subject_by_object_sour... \n", "66 mapping_statement_count_subject_by_object_sour... \n", "67 mapping_statement_count_subject_by_object_sour... \n", "68 mapping_statement_count_subject_by_object_sour... \n", "69 mapping_statement_count_subject_by_object_sour... \n", "70 mapping_statement_count_subject_by_object_sour... \n", "71 mapping_statement_count_subject_by_object_sour... \n", "72 mapping_statement_count_subject_by_object_sour... \n", "73 mapping_statement_count_subject_by_object_sour... \n", "74 mapping_statement_count_subject_by_object_sour... \n", "75 mapping_statement_count_subject_by_object_sour... \n", "76 mapping_statement_count_subject_by_object_sour... \n", "77 mapping_statement_count_subject_by_object_sour... \n", "78 mapping_statement_count_subject_by_object_sour... \n", "79 mapping_statement_count_subject_by_object_sour... \n", "80 mapping_statement_count_subject_by_object_sour... \n", "81 mapping_statement_count_subject_by_object_sour... \n", "82 mapping_statement_count_subject_by_object_sour... \n", "83 was_generated_by_started_at_time \n", "84 was_generated_by_was_associated_with \n", "85 was_generated_by_acted_on_behalf_of \n", "86 ontologies_id \n", "87 ontologies_version \n", "88 ontologies_version_info \n", "\n", " value \n", "0 AllOntologies \n", "1 [] \n", "2 [] \n", "3 1440 \n", "4 53 \n", "5 1387 \n", "6 1374 \n", "7 66 \n", "8 4 \n", "9 0 \n", "10 0 \n", "11 0 \n", "12 15642 \n", "13 2842 \n", "14 584 \n", "15 {} \n", "16 4391 \n", "17 4391 \n", "18 {} \n", "19 {'http://orcid.org/0000-0001-7941-2961': Contr... \n", "20 {} \n", "21 0 \n", "22 0 \n", "23 8 \n", "24 20 \n", "25 134 \n", "26 9 \n", "27 76 \n", "28 441 \n", "29 2154 \n", "30 25 \n", "31 4250 \n", "32 97 \n", "33 19 \n", "34 554 \n", "35 8 \n", "36 330 \n", "37 2 \n", "38 1 \n", "39 4 \n", "40 2 \n", "41 5 \n", "42 5 \n", "43 134 \n", "44 20 \n", "45 15 \n", "46 1 \n", "47 4 \n", "48 3 \n", "49 11 \n", "50 1 \n", "51 1 \n", "52 6 \n", "53 5 \n", "54 1 \n", "55 4 \n", "56 2 \n", "57 1 \n", "58 1 \n", "59 8 \n", "60 321 \n", "61 2 \n", "62 1 \n", "63 4 \n", "64 2 \n", "65 5 \n", "66 5 \n", "67 133 \n", "68 20 \n", "69 15 \n", "70 1 \n", "71 4 \n", "72 3 \n", "73 11 \n", "74 1 \n", "75 1 \n", "76 6 \n", "77 5 \n", "78 1 \n", "79 4 \n", "80 2 \n", "81 1 \n", "82 1 \n", "83 2023-01-29T12:44:00.348450 \n", "84 OAK \n", "85 cjm \n", "86 obo:maxo.owl \n", "87 obo:maxo/releases/2022-12-19/maxo.owl \n", "88 2022-12-19 " ] }, "execution_count": 34, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df.melt()" ] }, { "cell_type": "markdown", "id": "a8220875", "metadata": {}, "source": [ "Note that the original YAML report included many \"nested\" summaries, where counts were broken down by a facet - e.g. edge counts:\n", "\n", "```yaml\n", "edge_count_by_predicate:\n", " BFO:0000051:\n", " facet: BFO:0000051\n", " filtered_count: 8\n", " MAXO:0000521:\n", " facet: MAXO:0000521\n", " filtered_count: 20\n", " MAXO:0000864:\n", " facet: MAXO:0000864\n", " filtered_count: 134\n", "...\n", "```\n", "\n", "These get flattened (\"denormalized\") in the conversion to TSV, creating a new column for each facet, but this isn't done for all objects since this would make too wide a table (e.g. the contributor report, some ontologies may have 100s of contributors).\n", "\n", "E.g.\n", "\n", "|variable|value|\n", "|---|---|\n", "|edge_count_by_predicate_BFO:0000051 | 8 | \n", "|edge_count_by_predicate_MAXO:0000521 | 20 |\n", "|edge_count_by_predicate_MAXO:0000864 | 134 |\n", "\n", "The fields names may be verbose but they are intended to be unambiguous. One problem with ontology stats reporting is that there is often built in ambiguity; e.g what does \"number of terms\" mean?\n", "\n", "- number of classes\n", "- number of classes plus relations (object properties?)\n", "- are obsolete classes included? what about merged classes?\n", "\n", "If you want to look up documentation for any of these fields, just prefix with `https://incatools.github.io/ontology-access-kit/datamodels/summary-statistics/`\n", "\n", "E.g. https://incatools.github.io/ontology-access-kit/datamodels/summary-statistics/non_deprecated_class_count.html\n", "\n", "(in future these elements may have their own w3id URIs)\n", "\n", "Note this only works for \"non-denormalized\" fields - to interpret \"edge_count_by_predicate_BFO:0000051\" you must split this into the base statistic `edge_count_by_predicate` and the entity (BFO:0000051, aka has-part). Or you can simply look at the native normalized YAML output.\n", "\n", "## Summarizing by branches\n", "\n", "We can pass in a list of branches:" ] }, { "cell_type": "code", "execution_count": 29, "id": "fc330b1d", "metadata": {}, "outputs": [], "source": [ "maxo statistics --has-prefix MAXO -O csv -o output/maxo-stats-roots.tsv MAXO:0000001 MAXO:0000058 MAXO:0000002 MAXO:0000003 MAXO:0000013 MAXO:0000017 MAXO:0000021 MAXO:0001014" ] }, { "cell_type": "markdown", "id": "02a2d4c1", "metadata": {}, "source": [ "You can download this: [output/maxo-stats-roots.tsv](output/maxo-stats-roots.tsv) and use excel etc to view.\n", "\n", "Or see [this google sheet](https://docs.google.com/spreadsheets/d/1sKP7hhsY9YAVKEnLBqM6Zef_O80uOj6QPEvCuPYhrow/edit?usp=sharing)\n" ] }, { "cell_type": "code", "execution_count": 37, "id": "61ca3d14", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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idcompared_withagentsclass_countdeprecated_class_countnon_deprecated_class_countclass_count_with_text_definitionsclass_count_without_text_definitionsobject_property_countannotation_property_countnamed_individual_countsubset_countrdf_triple_countsubclass_of_axiom_countequivalent_classes_axiom_countentailed_edge_count_by_predicatedistinct_synonym_countsynonym_statement_countclass_count_by_categorycontributor_summarychange_summarymerged_class_querydeprecated_property_countedge_count_by_predicate_BFO:0000051edge_count_by_predicate_MAXO:0000521edge_count_by_predicate_MAXO:0000864edge_count_by_predicate_MAXO:0001015edge_count_by_predicate_MAXO:0001027edge_count_by_predicate_RO:0002233edge_count_by_predicate_rdfs:subClassOfsynonym_statement_count_by_predicate_hasBroadSynonymsynonym_statement_count_by_predicate_hasExactSynonymsynonym_statement_count_by_predicate_hasNarrowSynonymsynonym_statement_count_by_predicate_hasRelatedSynonymmapping_statement_count_by_predicate_hasDbXrefmapping_statement_count_by_object_source_OGMSmapping_statement_count_by_object_source_NCITmapping_statement_count_by_object_source_OAEmapping_statement_count_by_object_source_SIOmapping_statement_count_by_object_source_EROmapping_statement_count_by_object_source_NCROmapping_statement_count_by_object_source_SCDOmapping_statement_count_by_object_source_OMITmapping_statement_count_by_object_source_CHEBImapping_statement_count_by_object_source_MeSHmapping_statement_count_by_object_source_OBImapping_statement_count_by_object_source_IDOmapping_statement_count_by_object_source_VOmapping_statement_count_by_object_source_httpsmapping_statement_count_by_object_source_PMIDmapping_statement_count_by_object_source_NCItmapping_statement_count_by_object_source_UMLS_CUImapping_statement_count_by_object_source_CMOmapping_statement_count_by_object_source_NCBIBookmapping_statement_count_by_object_source_MMOmapping_statement_count_by_object_source_VSOmapping_statement_count_by_object_source_httpmapping_statement_count_by_object_source_EFOmapping_statement_count_by_object_source_IDOMALmapping_statement_count_subject_by_object_source_OGMSmapping_statement_count_subject_by_object_source_NCITmapping_statement_count_subject_by_object_source_OAEmapping_statement_count_subject_by_object_source_SIOmapping_statement_count_subject_by_object_source_EROmapping_statement_count_subject_by_object_source_NCROmapping_statement_count_subject_by_object_source_SCDOmapping_statement_count_subject_by_object_source_OMITmapping_statement_count_subject_by_object_source_CHEBImapping_statement_count_subject_by_object_source_MeSHmapping_statement_count_subject_by_object_source_OBImapping_statement_count_subject_by_object_source_IDOmapping_statement_count_subject_by_object_source_VOmapping_statement_count_subject_by_object_source_httpsmapping_statement_count_subject_by_object_source_PMIDmapping_statement_count_subject_by_object_source_NCItmapping_statement_count_subject_by_object_source_UMLS_CUImapping_statement_count_subject_by_object_source_CMOmapping_statement_count_subject_by_object_source_NCBIBookmapping_statement_count_subject_by_object_source_MMOmapping_statement_count_subject_by_object_source_VSOmapping_statement_count_subject_by_object_source_httpmapping_statement_count_subject_by_object_source_EFOmapping_statement_count_subject_by_object_source_IDOMAL
0medical action[][]1387013871374130000153552789584{}43854385{}{'http://orcid.org/0000-0001-7941-2961': Contr...{}008.020.0134.09.076.0441.0210125.0424697.017.0553.08.0329.02.01.04.02.05.05.0134.019.015.01.04.03.011.01.01.06.05.01.04.02.01.01.08.0320.02.01.04.02.05.05.0133.019.015.01.04.03.011.01.01.06.05.01.04.02.01.01.0
1pharmacotherapy[][]2560256248800003772556134{}15531553{}{'http://orcid.org/0000-0001-7941-2961': Contr...{}00134.042212.0151519.07.0196.01.057.01.01.0134.02.01.01.056.01.01.0133.02.01.0
2therapeutic procedure[][]8980898885130000105551853394{}33633363{}{'http://orcid.org/0000-0001-7941-2961': Contr...{}009.0134.076.0260.0137424.0326265.012.0386.06.0203.02.01.04.02.03.04.0134.019.01.03.06.01.01.02.02.06.0195.02.01.04.02.03.04.0133.019.01.03.06.01.01.02.02.0
3diagnostic procedure[][]55605565560000058881140254{}14921492{}{'http://orcid.org/0000-0001-7941-2961': Contr...{}008.0246.08862.0145232.06.0180.01.0151.01.012.05.06.03.01.04.01.0150.01.012.05.06.03.01.04.0
4complementary and alternative medical therapy[][]6066000005360{}99{}{'<http://orcid.org/0000-0001-7941-2961>': Con...{}00672.08.06.02.06.02.0
5preventative therapeutics[][]220222200000206341{}4646{}{'http://orcid.org/0000-0001-7941-2961': Contr...{}0011.0234614.06.02.01.04.01.01.06.02.01.04.01.01.0
6palliative care[][]6066000005980{}1515{}{'<http://orcid.org/0000-0001-7941-2961>': Con...{}00878.06.05.01.04.01.0
7medical action avoidance[][]90990000081180{}1818{}{'http://orcid.org/0000-0001-7941-2961': Contr...{}009.0918
\n", "
" ], "text/plain": [ " id compared_with agents \\\n", "0 medical action [] [] \n", "1 pharmacotherapy [] [] \n", "2 therapeutic procedure [] [] \n", "3 diagnostic procedure [] [] \n", "4 complementary and alternative medical therapy [] [] \n", "5 preventative therapeutics [] [] \n", "6 palliative care [] [] \n", "7 medical action avoidance [] [] \n", "\n", " class_count deprecated_class_count non_deprecated_class_count \\\n", "0 1387 0 1387 \n", "1 256 0 256 \n", "2 898 0 898 \n", "3 556 0 556 \n", "4 6 0 6 \n", "5 22 0 22 \n", "6 6 0 6 \n", "7 9 0 9 \n", "\n", " class_count_with_text_definitions class_count_without_text_definitions \\\n", "0 1374 13 \n", "1 248 8 \n", "2 885 13 \n", "3 556 0 \n", "4 6 0 \n", "5 22 0 \n", "6 6 0 \n", "7 9 0 \n", "\n", " object_property_count annotation_property_count named_individual_count \\\n", "0 0 0 0 \n", "1 0 0 0 \n", "2 0 0 0 \n", "3 0 0 0 \n", "4 0 0 0 \n", "5 0 0 0 \n", "6 0 0 0 \n", "7 0 0 0 \n", "\n", " subset_count rdf_triple_count subclass_of_axiom_count \\\n", "0 0 15355 2789 \n", "1 0 3772 556 \n", "2 0 10555 1853 \n", "3 0 5888 1140 \n", "4 0 53 6 \n", "5 0 206 34 \n", "6 0 59 8 \n", "7 0 81 18 \n", "\n", " equivalent_classes_axiom_count entailed_edge_count_by_predicate \\\n", "0 584 {} \n", "1 134 {} \n", "2 394 {} \n", "3 254 {} \n", "4 0 {} \n", "5 1 {} \n", "6 0 {} \n", "7 0 {} \n", "\n", " distinct_synonym_count synonym_statement_count class_count_by_category \\\n", "0 4385 4385 {} \n", "1 1553 1553 {} \n", "2 3363 3363 {} \n", "3 1492 1492 {} \n", "4 9 9 {} \n", "5 46 46 {} \n", "6 15 15 {} \n", "7 18 18 {} \n", "\n", " contributor_summary change_summary \\\n", "0 {'http://orcid.org/0000-0001-7941-2961': Contr... {} \n", "1 {'http://orcid.org/0000-0001-7941-2961': Contr... {} \n", "2 {'http://orcid.org/0000-0001-7941-2961': Contr... {} \n", "3 {'http://orcid.org/0000-0001-7941-2961': Contr... {} \n", "4 {'': Con... {} \n", "5 {'http://orcid.org/0000-0001-7941-2961': Contr... {} \n", "6 {'': Con... {} \n", "7 {'http://orcid.org/0000-0001-7941-2961': Contr... {} \n", "\n", " merged_class_query deprecated_property_count \\\n", "0 0 0 \n", "1 0 0 \n", "2 0 0 \n", "3 0 0 \n", "4 0 0 \n", "5 0 0 \n", "6 0 0 \n", "7 0 0 \n", "\n", " edge_count_by_predicate_BFO:0000051 edge_count_by_predicate_MAXO:0000521 \\\n", "0 8.0 20.0 \n", "1 \n", "2 9.0 \n", "3 8.0 \n", "4 \n", "5 11.0 \n", "6 \n", "7 \n", "\n", " edge_count_by_predicate_MAXO:0000864 edge_count_by_predicate_MAXO:0001015 \\\n", "0 134.0 9.0 \n", "1 134.0 \n", "2 134.0 \n", "3 \n", "4 \n", "5 \n", "6 \n", "7 9.0 \n", "\n", " edge_count_by_predicate_MAXO:0001027 edge_count_by_predicate_RO:0002233 \\\n", "0 76.0 441.0 \n", "1 \n", "2 76.0 260.0 \n", "3 246.0 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " edge_count_by_predicate_rdfs:subClassOf \\\n", "0 2101 \n", "1 422 \n", "2 1374 \n", "3 886 \n", "4 6 \n", "5 23 \n", "6 8 \n", "7 9 \n", "\n", " synonym_statement_count_by_predicate_hasBroadSynonym \\\n", "0 25.0 \n", "1 12.0 \n", "2 24.0 \n", "3 2.0 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " synonym_statement_count_by_predicate_hasExactSynonym \\\n", "0 4246 \n", "1 1515 \n", "2 3262 \n", "3 1452 \n", "4 7 \n", "5 46 \n", "6 7 \n", "7 18 \n", "\n", " synonym_statement_count_by_predicate_hasNarrowSynonym \\\n", "0 97.0 \n", "1 19.0 \n", "2 65.0 \n", "3 32.0 \n", "4 2.0 \n", "5 \n", "6 8.0 \n", "7 \n", "\n", " synonym_statement_count_by_predicate_hasRelatedSynonym \\\n", "0 17.0 \n", "1 7.0 \n", "2 12.0 \n", "3 6.0 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_by_predicate_hasDbXref \\\n", "0 553.0 \n", "1 196.0 \n", "2 386.0 \n", "3 180.0 \n", "4 8.0 \n", "5 14.0 \n", "6 6.0 \n", "7 \n", "\n", " mapping_statement_count_by_object_source_OGMS \\\n", "0 8.0 \n", "1 1.0 \n", "2 6.0 \n", "3 1.0 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_by_object_source_NCIT \\\n", "0 329.0 \n", "1 57.0 \n", "2 203.0 \n", "3 151.0 \n", "4 6.0 \n", "5 6.0 \n", "6 5.0 \n", "7 \n", "\n", " mapping_statement_count_by_object_source_OAE \\\n", "0 2.0 \n", "1 \n", "2 2.0 \n", "3 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_by_object_source_SIO \\\n", "0 1.0 \n", "1 \n", "2 1.0 \n", "3 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_by_object_source_ERO \\\n", "0 4.0 \n", "1 \n", "2 4.0 \n", "3 1.0 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_by_object_source_NCRO \\\n", "0 2.0 \n", "1 1.0 \n", "2 2.0 \n", "3 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_by_object_source_SCDO \\\n", "0 5.0 \n", "1 \n", "2 3.0 \n", "3 \n", "4 2.0 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_by_object_source_OMIT \\\n", "0 5.0 \n", "1 1.0 \n", "2 4.0 \n", "3 \n", "4 \n", "5 \n", "6 1.0 \n", "7 \n", "\n", " mapping_statement_count_by_object_source_CHEBI \\\n", "0 134.0 \n", "1 134.0 \n", "2 134.0 \n", "3 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_by_object_source_MeSH \\\n", "0 19.0 \n", "1 \n", "2 19.0 \n", "3 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_by_object_source_OBI \\\n", "0 15.0 \n", "1 \n", "2 1.0 \n", "3 12.0 \n", "4 \n", "5 2.0 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_by_object_source_IDO \\\n", "0 1.0 \n", "1 \n", "2 \n", "3 \n", "4 \n", "5 1.0 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_by_object_source_VO \\\n", "0 4.0 \n", "1 \n", "2 \n", "3 \n", "4 \n", "5 4.0 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_by_object_source_https \\\n", "0 3.0 \n", "1 2.0 \n", "2 3.0 \n", "3 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_by_object_source_PMID \\\n", "0 11.0 \n", "1 1.0 \n", "2 6.0 \n", "3 5.0 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_by_object_source_NCIt \\\n", "0 1.0 \n", "1 \n", "2 1.0 \n", "3 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_by_object_source_UMLS_CUI \\\n", "0 1.0 \n", "1 \n", "2 1.0 \n", "3 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_by_object_source_CMO \\\n", "0 6.0 \n", "1 \n", "2 \n", "3 6.0 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_by_object_source_NCBIBook \\\n", "0 5.0 \n", "1 \n", "2 2.0 \n", "3 3.0 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_by_object_source_MMO \\\n", "0 1.0 \n", "1 \n", "2 \n", "3 1.0 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_by_object_source_VSO \\\n", "0 4.0 \n", "1 \n", "2 \n", "3 4.0 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_by_object_source_http \\\n", "0 2.0 \n", "1 \n", "2 2.0 \n", "3 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_by_object_source_EFO \\\n", "0 1.0 \n", "1 \n", "2 \n", "3 \n", "4 \n", "5 1.0 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_by_object_source_IDOMAL \\\n", "0 1.0 \n", "1 \n", "2 \n", "3 \n", "4 \n", "5 1.0 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_subject_by_object_source_OGMS \\\n", "0 8.0 \n", "1 1.0 \n", "2 6.0 \n", "3 1.0 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_subject_by_object_source_NCIT \\\n", "0 320.0 \n", "1 56.0 \n", "2 195.0 \n", "3 150.0 \n", "4 6.0 \n", "5 6.0 \n", "6 4.0 \n", "7 \n", "\n", " mapping_statement_count_subject_by_object_source_OAE \\\n", "0 2.0 \n", "1 \n", "2 2.0 \n", "3 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_subject_by_object_source_SIO \\\n", "0 1.0 \n", "1 \n", "2 1.0 \n", "3 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_subject_by_object_source_ERO \\\n", "0 4.0 \n", "1 \n", "2 4.0 \n", "3 1.0 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_subject_by_object_source_NCRO \\\n", "0 2.0 \n", "1 1.0 \n", "2 2.0 \n", "3 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_subject_by_object_source_SCDO \\\n", "0 5.0 \n", "1 \n", "2 3.0 \n", "3 \n", "4 2.0 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_subject_by_object_source_OMIT \\\n", "0 5.0 \n", "1 1.0 \n", "2 4.0 \n", "3 \n", "4 \n", "5 \n", "6 1.0 \n", "7 \n", "\n", " mapping_statement_count_subject_by_object_source_CHEBI \\\n", "0 133.0 \n", "1 133.0 \n", "2 133.0 \n", "3 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_subject_by_object_source_MeSH \\\n", "0 19.0 \n", "1 \n", "2 19.0 \n", "3 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_subject_by_object_source_OBI \\\n", "0 15.0 \n", "1 \n", "2 1.0 \n", "3 12.0 \n", "4 \n", "5 2.0 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_subject_by_object_source_IDO \\\n", "0 1.0 \n", "1 \n", "2 \n", "3 \n", "4 \n", "5 1.0 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_subject_by_object_source_VO \\\n", "0 4.0 \n", "1 \n", "2 \n", "3 \n", "4 \n", "5 4.0 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_subject_by_object_source_https \\\n", "0 3.0 \n", "1 2.0 \n", "2 3.0 \n", "3 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_subject_by_object_source_PMID \\\n", "0 11.0 \n", "1 1.0 \n", "2 6.0 \n", "3 5.0 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_subject_by_object_source_NCIt \\\n", "0 1.0 \n", "1 \n", "2 1.0 \n", "3 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_subject_by_object_source_UMLS_CUI \\\n", "0 1.0 \n", "1 \n", "2 1.0 \n", "3 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_subject_by_object_source_CMO \\\n", "0 6.0 \n", "1 \n", "2 \n", "3 6.0 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_subject_by_object_source_NCBIBook \\\n", "0 5.0 \n", "1 \n", "2 2.0 \n", "3 3.0 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_subject_by_object_source_MMO \\\n", "0 1.0 \n", "1 \n", "2 \n", "3 1.0 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_subject_by_object_source_VSO \\\n", "0 4.0 \n", "1 \n", "2 \n", "3 4.0 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_subject_by_object_source_http \\\n", "0 2.0 \n", "1 \n", "2 2.0 \n", "3 \n", "4 \n", "5 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_subject_by_object_source_EFO \\\n", "0 1.0 \n", "1 \n", "2 \n", "3 \n", "4 \n", "5 1.0 \n", "6 \n", "7 \n", "\n", " mapping_statement_count_subject_by_object_source_IDOMAL \n", "0 1.0 \n", "1 \n", "2 \n", "3 \n", "4 \n", "5 1.0 \n", "6 \n", "7 " ] }, "execution_count": 37, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df = pd.read_csv(\"output/maxo-stats-roots.tsv\", sep=\"\\t\").fillna(\"\")\n", "df" ] }, { "cell_type": "markdown", "id": "28984bd2", "metadata": {}, "source": [ "Here each row is a branch (note that numbers are cumulative, so numbers for a parent include\n", "numbers for children, even if there is a separate row for that child).\n", "\n", "Note that you will never see deprecated classes when using this option, if the deprecated classes are not in the hierarchy (as is conventional for OBO ontologies)\n", "\n", "We may prefer to view the transposed form:" ] }, { "cell_type": "code", "execution_count": 38, "id": "47e9ac06", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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non_deprecated_class_count138725689855662269
class_count_with_text_definitions137424888555662269
class_count_without_text_definitions1381300000
object_property_count00000000
annotation_property_count00000000
named_individual_count00000000
subset_count00000000
rdf_triple_count153553772105555888532065981
subclass_of_axiom_count278955618531140634818
equivalent_classes_axiom_count5841343942540100
entailed_edge_count_by_predicate{}{}{}{}{}{}{}{}
distinct_synonym_count43851553336314929461518
synonym_statement_count43851553336314929461518
class_count_by_category{}{}{}{}{}{}{}{}
contributor_summary{'http://orcid.org/0000-0001-7941-2961': Contr...{'http://orcid.org/0000-0001-7941-2961': Contr...{'http://orcid.org/0000-0001-7941-2961': Contr...{'http://orcid.org/0000-0001-7941-2961': Contr...{'<http://orcid.org/0000-0001-7941-2961>': Con...{'http://orcid.org/0000-0001-7941-2961': Contr...{'<http://orcid.org/0000-0001-7941-2961>': Con...{'http://orcid.org/0000-0001-7941-2961': Contr...
change_summary{}{}{}{}{}{}{}{}
merged_class_query00000000
deprecated_property_count00000000
edge_count_by_predicate_BFO:00000518.08.0
edge_count_by_predicate_MAXO:000052120.09.011.0
edge_count_by_predicate_MAXO:0000864134.0134.0134.0
edge_count_by_predicate_MAXO:00010159.09.0
edge_count_by_predicate_MAXO:000102776.076.0
edge_count_by_predicate_RO:0002233441.0260.0246.0
edge_count_by_predicate_rdfs:subClassOf2101422137488662389
synonym_statement_count_by_predicate_hasBroadSynonym25.012.024.02.0
synonym_statement_count_by_predicate_hasExactSynonym4246151532621452746718
synonym_statement_count_by_predicate_hasNarrowSynonym97.019.065.032.02.08.0
synonym_statement_count_by_predicate_hasRelatedSynonym17.07.012.06.0
mapping_statement_count_by_predicate_hasDbXref553.0196.0386.0180.08.014.06.0
mapping_statement_count_by_object_source_OGMS8.01.06.01.0
mapping_statement_count_by_object_source_NCIT329.057.0203.0151.06.06.05.0
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"mapping_statement_count_by_object_source_https \n", "mapping_statement_count_by_object_source_PMID \n", "mapping_statement_count_by_object_source_NCIt \n", "mapping_statement_count_by_object_source_UMLS_CUI \n", "mapping_statement_count_by_object_source_CMO \n", "mapping_statement_count_by_object_source_NCBIBook \n", "mapping_statement_count_by_object_source_MMO \n", "mapping_statement_count_by_object_source_VSO \n", "mapping_statement_count_by_object_source_http \n", "mapping_statement_count_by_object_source_EFO \n", "mapping_statement_count_by_object_source_IDOMAL \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... 6.0 \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... 2.0 \n", 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"mapping_statement_count_by_object_source_IDO 1.0 \n", "mapping_statement_count_by_object_source_VO 4.0 \n", "mapping_statement_count_by_object_source_https \n", "mapping_statement_count_by_object_source_PMID \n", "mapping_statement_count_by_object_source_NCIt \n", "mapping_statement_count_by_object_source_UMLS_CUI \n", "mapping_statement_count_by_object_source_CMO \n", "mapping_statement_count_by_object_source_NCBIBook \n", "mapping_statement_count_by_object_source_MMO \n", "mapping_statement_count_by_object_source_VSO \n", "mapping_statement_count_by_object_source_http \n", "mapping_statement_count_by_object_source_EFO 1.0 \n", "mapping_statement_count_by_object_source_IDOMAL 1.0 \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... 6.0 \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", 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"edge_count_by_predicate_MAXO:0001015 \n", "edge_count_by_predicate_MAXO:0001027 \n", "edge_count_by_predicate_RO:0002233 \n", "edge_count_by_predicate_rdfs:subClassOf 8 \n", "synonym_statement_count_by_predicate_hasBroadSy... \n", "synonym_statement_count_by_predicate_hasExactSy... 7 \n", "synonym_statement_count_by_predicate_hasNarrowS... 8.0 \n", "synonym_statement_count_by_predicate_hasRelated... \n", "mapping_statement_count_by_predicate_hasDbXref 6.0 \n", "mapping_statement_count_by_object_source_OGMS \n", "mapping_statement_count_by_object_source_NCIT 5.0 \n", "mapping_statement_count_by_object_source_OAE \n", "mapping_statement_count_by_object_source_SIO \n", "mapping_statement_count_by_object_source_ERO \n", "mapping_statement_count_by_object_source_NCRO \n", "mapping_statement_count_by_object_source_SCDO \n", "mapping_statement_count_by_object_source_OMIT 1.0 \n", "mapping_statement_count_by_object_source_CHEBI \n", "mapping_statement_count_by_object_source_MeSH \n", "mapping_statement_count_by_object_source_OBI \n", "mapping_statement_count_by_object_source_IDO \n", "mapping_statement_count_by_object_source_VO \n", "mapping_statement_count_by_object_source_https \n", "mapping_statement_count_by_object_source_PMID \n", "mapping_statement_count_by_object_source_NCIt \n", "mapping_statement_count_by_object_source_UMLS_CUI \n", "mapping_statement_count_by_object_source_CMO \n", "mapping_statement_count_by_object_source_NCBIBook \n", "mapping_statement_count_by_object_source_MMO \n", "mapping_statement_count_by_object_source_VSO \n", "mapping_statement_count_by_object_source_http \n", "mapping_statement_count_by_object_source_EFO \n", "mapping_statement_count_by_object_source_IDOMAL \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... 4.0 \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... 1.0 \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "\n", " 7 \n", "id medical action avoidance \n", "compared_with [] \n", "agents [] \n", "class_count 9 \n", "deprecated_class_count 0 \n", "non_deprecated_class_count 9 \n", "class_count_with_text_definitions 9 \n", "class_count_without_text_definitions 0 \n", "object_property_count 0 \n", "annotation_property_count 0 \n", "named_individual_count 0 \n", "subset_count 0 \n", "rdf_triple_count 81 \n", "subclass_of_axiom_count 18 \n", "equivalent_classes_axiom_count 0 \n", "entailed_edge_count_by_predicate {} \n", "distinct_synonym_count 18 \n", "synonym_statement_count 18 \n", "class_count_by_category {} \n", "contributor_summary {'http://orcid.org/0000-0001-7941-2961': Contr... \n", "change_summary {} \n", "merged_class_query 0 \n", "deprecated_property_count 0 \n", "edge_count_by_predicate_BFO:0000051 \n", "edge_count_by_predicate_MAXO:0000521 \n", "edge_count_by_predicate_MAXO:0000864 \n", "edge_count_by_predicate_MAXO:0001015 9.0 \n", "edge_count_by_predicate_MAXO:0001027 \n", "edge_count_by_predicate_RO:0002233 \n", "edge_count_by_predicate_rdfs:subClassOf 9 \n", "synonym_statement_count_by_predicate_hasBroadSy... \n", "synonym_statement_count_by_predicate_hasExactSy... 18 \n", "synonym_statement_count_by_predicate_hasNarrowS... \n", "synonym_statement_count_by_predicate_hasRelated... \n", "mapping_statement_count_by_predicate_hasDbXref \n", "mapping_statement_count_by_object_source_OGMS \n", "mapping_statement_count_by_object_source_NCIT \n", "mapping_statement_count_by_object_source_OAE \n", "mapping_statement_count_by_object_source_SIO \n", "mapping_statement_count_by_object_source_ERO \n", "mapping_statement_count_by_object_source_NCRO \n", "mapping_statement_count_by_object_source_SCDO \n", "mapping_statement_count_by_object_source_OMIT \n", "mapping_statement_count_by_object_source_CHEBI \n", "mapping_statement_count_by_object_source_MeSH \n", "mapping_statement_count_by_object_source_OBI \n", "mapping_statement_count_by_object_source_IDO \n", "mapping_statement_count_by_object_source_VO \n", "mapping_statement_count_by_object_source_https \n", "mapping_statement_count_by_object_source_PMID \n", "mapping_statement_count_by_object_source_NCIt \n", "mapping_statement_count_by_object_source_UMLS_CUI \n", "mapping_statement_count_by_object_source_CMO \n", "mapping_statement_count_by_object_source_NCBIBook \n", "mapping_statement_count_by_object_source_MMO \n", "mapping_statement_count_by_object_source_VSO \n", "mapping_statement_count_by_object_source_http \n", "mapping_statement_count_by_object_source_EFO \n", "mapping_statement_count_by_object_source_IDOMAL \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... \n", "mapping_statement_count_subject_by_object_sourc... " ] }, "execution_count": 38, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df.convert_dtypes().transpose()" ] }, { "cell_type": "markdown", "id": "bca61839", "metadata": {}, "source": [ "Note that the categories are not disjoint - some terms can be in more than one branch, and \"medical action\"\n", "covers everything.\n", "\n", "\n", "## Exploring mappings\n", "\n", "Next let's use OAK to query mappings in MAXO. There are a lot, so for exploration purposes let's fetch this for all terms that have the string \"biopsy\" in them:" ] }, { "cell_type": "code", "execution_count": 39, "id": "d7d81f61", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "# curie_map: {}\r\n", "# license: UNSPECIFIED\r\n", "# mapping_set_id: temp\r\n", "subject_id\tsubject_label\tpredicate_id\tobject_id\tobject_label\tmapping_justification\tsubject_source\tobject_source\r\n", "MAXO:0000332\tbiopsy of anus\toio:hasDbXref\tNCIT:C51586\t\tsemapv:UnspecifiedMatching\tMAXO\tNCIT\r\n", "MAXO:0001269\tclinical biopsy\toio:hasDbXref\tOBI:0002650\tbiopsy\tsemapv:UnspecifiedMatching\tMAXO\tOBI\r\n", "MAXO:0001269\tclinical biopsy\toio:hasDbXref\tOBI:0002650\tbiopsy\tsemapv:UnspecifiedMatching\tMAXO\tOBI\r\n", "MAXO:0001270\tclinical computed tomography assisted biopsy\toio:hasDbXref\tOBI:0002652\tcomputed tomography assisted biopsy\tsemapv:UnspecifiedMatching\tMAXO\tOBI\r\n", "MAXO:0001270\tclinical computed tomography assisted biopsy\toio:hasDbXref\tOBI:0002652\tcomputed tomography assisted biopsy\tsemapv:UnspecifiedMatching\tMAXO\tOBI\r\n", "MAXO:0001271\tclinical core needle biopsy\toio:hasDbXref\tOBI:0002656\tcore needle biopsy\tsemapv:UnspecifiedMatching\tMAXO\tOBI\r\n", "MAXO:0001271\tclinical core needle biopsy\toio:hasDbXref\tOBI:0002656\tcore needle biopsy\tsemapv:UnspecifiedMatching\tMAXO\tOBI\r\n", "MAXO:0001272\tclinical fine needle aspiration biopsy\toio:hasDbXref\tOBI:0002655\tfine needle aspiration biopsy\tsemapv:UnspecifiedMatching\tMAXO\tOBI\r\n", "MAXO:0001272\tclinical fine needle aspiration biopsy\toio:hasDbXref\tOBI:0002655\tfine needle aspiration biopsy\tsemapv:UnspecifiedMatching\tMAXO\tOBI\r\n", "MAXO:0001273\tclinical image guided biopsy\toio:hasDbXref\tOBI:0002651\timage guided biopsy\tsemapv:UnspecifiedMatching\tMAXO\tOBI\r\n", "MAXO:0001273\tclinical image guided biopsy\toio:hasDbXref\tOBI:0002651\timage guided biopsy\tsemapv:UnspecifiedMatching\tMAXO\tOBI\r\n", "MAXO:0001274\tclinical needle biopsy\toio:hasDbXref\tOBI:0002654\tneedle biopsy\tsemapv:UnspecifiedMatching\tMAXO\tOBI\r\n", "MAXO:0001274\tclinical needle biopsy\toio:hasDbXref\tOBI:0002654\tneedle biopsy\tsemapv:UnspecifiedMatching\tMAXO\tOBI\r\n", "MAXO:0001275\tclinical surgical biopsy\toio:hasDbXref\tOBI:0002657\tsurgical biopsy\tsemapv:UnspecifiedMatching\tMAXO\tOBI\r\n", "MAXO:0001275\tclinical surgical biopsy\toio:hasDbXref\tOBI:0002657\tsurgical biopsy\tsemapv:UnspecifiedMatching\tMAXO\tOBI\r\n", "MAXO:0001276\tclinical ultrasound-guided needle biopsy\toio:hasDbXref\tOBI:0002653\tultrasound-guided needle biopsy\tsemapv:UnspecifiedMatching\tMAXO\tOBI\r\n", "MAXO:0001276\tclinical ultrasound-guided needle biopsy\toio:hasDbXref\tOBI:0002653\tultrasound-guided needle biopsy\tsemapv:UnspecifiedMatching\tMAXO\tOBI\r\n", "\r\n" ] } ], "source": [ "maxo mappings l~biopsy -O sssom" ] }, { "cell_type": "code", "execution_count": 40, "id": "8a0326ef", "metadata": {}, "outputs": [], "source": [ "maxo mappings l~biopsy -O sssom -o output/maxo-biopsy.sssom.tsv" ] }, { "cell_type": "code", "execution_count": 41, "id": "a93c62f7", "metadata": {}, "outputs": [], "source": [ "df = pd.read_csv(\"output/maxo-biopsy.sssom.tsv\", sep=\"\\t\", comment=\"#\").fillna(\"\")" ] }, { "cell_type": "code", "execution_count": 42, "id": "0ba8b616", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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subject_idsubject_labelpredicate_idobject_idobject_labelmapping_justificationsubject_sourceobject_source
0MAXO:0000332biopsy of anusoio:hasDbXrefNCIT:C51586semapv:UnspecifiedMatchingMAXONCIT
1MAXO:0001269clinical biopsyoio:hasDbXrefOBI:0002650biopsysemapv:UnspecifiedMatchingMAXOOBI
2MAXO:0001269clinical biopsyoio:hasDbXrefOBI:0002650biopsysemapv:UnspecifiedMatchingMAXOOBI
3MAXO:0001270clinical computed tomography assisted biopsyoio:hasDbXrefOBI:0002652computed tomography assisted biopsysemapv:UnspecifiedMatchingMAXOOBI
4MAXO:0001270clinical computed tomography assisted biopsyoio:hasDbXrefOBI:0002652computed tomography assisted biopsysemapv:UnspecifiedMatchingMAXOOBI
5MAXO:0001271clinical core needle biopsyoio:hasDbXrefOBI:0002656core needle biopsysemapv:UnspecifiedMatchingMAXOOBI
6MAXO:0001271clinical core needle biopsyoio:hasDbXrefOBI:0002656core needle biopsysemapv:UnspecifiedMatchingMAXOOBI
7MAXO:0001272clinical fine needle aspiration biopsyoio:hasDbXrefOBI:0002655fine needle aspiration biopsysemapv:UnspecifiedMatchingMAXOOBI
8MAXO:0001272clinical fine needle aspiration biopsyoio:hasDbXrefOBI:0002655fine needle aspiration biopsysemapv:UnspecifiedMatchingMAXOOBI
9MAXO:0001273clinical image guided biopsyoio:hasDbXrefOBI:0002651image guided biopsysemapv:UnspecifiedMatchingMAXOOBI
10MAXO:0001273clinical image guided biopsyoio:hasDbXrefOBI:0002651image guided biopsysemapv:UnspecifiedMatchingMAXOOBI
11MAXO:0001274clinical needle biopsyoio:hasDbXrefOBI:0002654needle biopsysemapv:UnspecifiedMatchingMAXOOBI
12MAXO:0001274clinical needle biopsyoio:hasDbXrefOBI:0002654needle biopsysemapv:UnspecifiedMatchingMAXOOBI
13MAXO:0001275clinical surgical biopsyoio:hasDbXrefOBI:0002657surgical biopsysemapv:UnspecifiedMatchingMAXOOBI
14MAXO:0001275clinical surgical biopsyoio:hasDbXrefOBI:0002657surgical biopsysemapv:UnspecifiedMatchingMAXOOBI
15MAXO:0001276clinical ultrasound-guided needle biopsyoio:hasDbXrefOBI:0002653ultrasound-guided needle biopsysemapv:UnspecifiedMatchingMAXOOBI
16MAXO:0001276clinical ultrasound-guided needle biopsyoio:hasDbXrefOBI:0002653ultrasound-guided needle biopsysemapv:UnspecifiedMatchingMAXOOBI
\n", "
" ], "text/plain": [ " subject_id subject_label predicate_id \\\n", "0 MAXO:0000332 biopsy of anus oio:hasDbXref \n", "1 MAXO:0001269 clinical biopsy oio:hasDbXref \n", "2 MAXO:0001269 clinical biopsy oio:hasDbXref \n", "3 MAXO:0001270 clinical computed tomography assisted biopsy oio:hasDbXref \n", "4 MAXO:0001270 clinical computed tomography assisted biopsy oio:hasDbXref \n", "5 MAXO:0001271 clinical core needle biopsy oio:hasDbXref \n", "6 MAXO:0001271 clinical core needle biopsy oio:hasDbXref \n", "7 MAXO:0001272 clinical fine needle aspiration biopsy oio:hasDbXref \n", "8 MAXO:0001272 clinical fine needle aspiration biopsy oio:hasDbXref \n", "9 MAXO:0001273 clinical image guided biopsy oio:hasDbXref \n", "10 MAXO:0001273 clinical image guided biopsy oio:hasDbXref \n", "11 MAXO:0001274 clinical needle biopsy oio:hasDbXref \n", "12 MAXO:0001274 clinical needle biopsy oio:hasDbXref \n", "13 MAXO:0001275 clinical surgical biopsy oio:hasDbXref \n", "14 MAXO:0001275 clinical surgical biopsy oio:hasDbXref \n", "15 MAXO:0001276 clinical ultrasound-guided needle biopsy oio:hasDbXref \n", "16 MAXO:0001276 clinical ultrasound-guided needle biopsy oio:hasDbXref \n", "\n", " object_id object_label \\\n", "0 NCIT:C51586 \n", "1 OBI:0002650 biopsy \n", "2 OBI:0002650 biopsy \n", "3 OBI:0002652 computed tomography assisted biopsy \n", "4 OBI:0002652 computed tomography assisted biopsy \n", "5 OBI:0002656 core needle biopsy \n", "6 OBI:0002656 core needle biopsy \n", "7 OBI:0002655 fine needle aspiration biopsy \n", "8 OBI:0002655 fine needle aspiration biopsy \n", "9 OBI:0002651 image guided biopsy \n", "10 OBI:0002651 image guided biopsy \n", "11 OBI:0002654 needle biopsy \n", "12 OBI:0002654 needle biopsy \n", "13 OBI:0002657 surgical biopsy \n", "14 OBI:0002657 surgical biopsy \n", "15 OBI:0002653 ultrasound-guided needle biopsy \n", "16 OBI:0002653 ultrasound-guided needle biopsy \n", "\n", " mapping_justification subject_source object_source \n", "0 semapv:UnspecifiedMatching MAXO NCIT \n", "1 semapv:UnspecifiedMatching MAXO OBI \n", "2 semapv:UnspecifiedMatching MAXO OBI \n", "3 semapv:UnspecifiedMatching MAXO OBI \n", "4 semapv:UnspecifiedMatching MAXO OBI \n", "5 semapv:UnspecifiedMatching MAXO OBI \n", "6 semapv:UnspecifiedMatching MAXO OBI \n", "7 semapv:UnspecifiedMatching MAXO OBI \n", "8 semapv:UnspecifiedMatching MAXO OBI \n", "9 semapv:UnspecifiedMatching MAXO OBI \n", "10 semapv:UnspecifiedMatching MAXO OBI \n", "11 semapv:UnspecifiedMatching MAXO OBI \n", "12 semapv:UnspecifiedMatching MAXO OBI \n", "13 semapv:UnspecifiedMatching MAXO OBI \n", "14 semapv:UnspecifiedMatching MAXO OBI \n", "15 semapv:UnspecifiedMatching MAXO OBI \n", "16 semapv:UnspecifiedMatching MAXO OBI " ] }, "execution_count": 42, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df" ] }, { "cell_type": "code", "execution_count": 44, "id": "e87451af", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "WARNING:root:Skipping as it is not a valid CURIE\r\n", "WARNING:root:Skipping as it is not a valid CURIE\r\n", "WARNING:root:Skipping as it is not a valid CURIE\r\n", "WARNING:root:Skipping as it is not a valid CURIE\r\n", "WARNING:root:Skipping as it is not a valid CURIE\r\n", "WARNING:root:Skipping as it is not a valid CURIE\r\n", "WARNING:root:Skipping as it is not a valid CURIE\r\n", "WARNING:root:Skipping as it is not a valid CURIE\r\n", "WARNING:root:Skipping as it is not a valid CURIE\r\n", "WARNING:root:Skipping as it is not a valid CURIE\r\n", "WARNING:root:Skipping as it is not a valid CURIE\r\n", "WARNING:root:Skipping as it is not a valid CURIE\r\n", "WARNING:root:Skipping as it is not a valid CURIE\r\n", "WARNING:root:Skipping as it is not a valid CURIE\r\n", "WARNING:root:Skipping as it is not a valid CURIE\r\n", "WARNING:root:Skipping as it is not a valid CURIE\r\n", "WARNING:root:Skipping as it is not a valid CURIE\r\n", "WARNING:root:Skipping as it is not a valid CURIE\r\n", "WARNING:root:Skipping as it is not a valid CURIE\r\n", "WARNING:root:Skipping as it is not a valid CURIE\r\n", "WARNING:root:Skipping as it is not a valid CURIE\r\n", "WARNING:root:Skipping as it is not a valid CURIE\r\n", "WARNING:root:Skipping as it is not a valid CURIE\r\n", "WARNING:root:Skipping as it is not a valid CURIE\r\n", "WARNING:root:Skipping as it is not a valid CURIE\r\n" ] } ], "source": [ "maxo -a sqlite:obo:ncit lexmatch l~biopsy -o output/maxo-lexmatch-ncit-biopsy.sssom.tsv" ] }, { "cell_type": "code", "execution_count": 45, "id": "89aee4da", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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subject_idsubject_labelpredicate_idobject_idobject_labelmapping_justificationmapping_toolconfidencesubject_match_fieldobject_match_fieldmatch_string
0MAXO:0000332biopsy of anusskos:closeMatchNCIT:C51586Biopsy of Anussemapv:LexicalMatchingoaklib0.5rdfs:labelrdfs:labelbiopsy of anus
1MAXO:0000332biopsy of anusskos:closeMatchNCIT:C51586Biopsy of Anussemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of anus
2MAXO:0000336biopsy of bone marrowskos:closeMatchNCIT:C15193Bone Marrow Biopsysemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of bone marrow
3MAXO:0000336biopsy of bone marrowskos:closeMatchNCIT:C15193Bone Marrow Biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymrdfs:labelbone marrow biopsy
4MAXO:0000336biopsy of bone marrowskos:closeMatchNCIT:C15193Bone Marrow Biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymoio:hasExactSynonymbone marrow biopsy
5MAXO:0000336biopsy of bone marrowskos:closeMatchNCIT:C15193Bone Marrow Biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymoio:hasExactSynonymbone marrow biopsy
6MAXO:0000338biopsy of brainskos:closeMatchNCIT:C51766Biopsy of Brainsemapv:LexicalMatchingoaklib0.5rdfs:labelrdfs:labelbiopsy of brain
7MAXO:0000338biopsy of brainskos:closeMatchNCIT:C51766Biopsy of Brainsemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of brain
8MAXO:0000338biopsy of brainskos:closeMatchNCIT:C51766Biopsy of Brainsemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymoio:hasExactSynonymbrain biopsy
9MAXO:0000340biopsy of breastskos:closeMatchNCIT:C51698Biopsy of Breastsemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of breast
10MAXO:0000340biopsy of breastskos:closeMatchNCIT:C51698Biopsy of Breastsemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymoio:hasExactSynonymbreast biopsy
11MAXO:0000340biopsy of breastskos:closeMatchNCIT:C51698Biopsy of Breastsemapv:LexicalMatchingoaklib0.5rdfs:labelrdfs:labelbiopsy of breast
12MAXO:0000341biopsy of bronchusskos:closeMatchNCIT:C51782Bronchial Biopsysemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of bronchus
13MAXO:0000350biopsy of colonskos:closeMatchNCIT:C51678Biopsy of Colonsemapv:LexicalMatchingoaklib0.5rdfs:labelrdfs:labelbiopsy of colon
14MAXO:0000350biopsy of colonskos:closeMatchNCIT:C51678Biopsy of Colonsemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of colon
15MAXO:0000355biopsy of duodenumskos:closeMatchNCIT:C51683Biopsy of Duodenumsemapv:LexicalMatchingoaklib0.5rdfs:labelrdfs:labelbiopsy of duodenum
16MAXO:0000355biopsy of duodenumskos:closeMatchNCIT:C51683Biopsy of Duodenumsemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of duodenum
17MAXO:0000359biopsy of esophagusskos:closeMatchNCIT:C51686Esophageal Biopsysemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of esophagus
18MAXO:0000366biopsy of heartskos:closeMatchNCIT:C51794Biopsy of Heartsemapv:LexicalMatchingoaklib0.5rdfs:labelrdfs:labelbiopsy of heart
19MAXO:0000366biopsy of heartskos:closeMatchNCIT:C51794Biopsy of Heartsemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of heart
20MAXO:0000373biopsy of larynxskos:closeMatchNCIT:C51663Biopsy of Larynxsemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of larynx
21MAXO:0000373biopsy of larynxskos:closeMatchNCIT:C51663Biopsy of Larynxsemapv:LexicalMatchingoaklib0.5rdfs:labelrdfs:labelbiopsy of larynx
22MAXO:0000375biopsy of lipskos:closeMatchNCIT:C51653Biopsy of Lipsemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of lip
23MAXO:0000375biopsy of lipskos:closeMatchNCIT:C51653Biopsy of Lipsemapv:LexicalMatchingoaklib0.5rdfs:labelrdfs:labelbiopsy of lip
24MAXO:0000376biopsy of liverskos:closeMatchNCIT:C51677Liver Biopsysemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of liver
25MAXO:0000376biopsy of liverskos:closeMatchNCIT:C51677Liver Biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymrdfs:labelliver biopsy
26MAXO:0000376biopsy of liverskos:closeMatchNCIT:C51677Liver Biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymoio:hasExactSynonymliver biopsy
27MAXO:0000380biopsy of lungskos:closeMatchNCIT:C51748Lung Biopsysemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of lung
28MAXO:0000380biopsy of lungskos:closeMatchNCIT:C51748Lung Biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymrdfs:labellung biopsy
29MAXO:0000380biopsy of lungskos:closeMatchNCIT:C51748Lung Biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymoio:hasExactSynonymlung biopsy
30MAXO:0000380biopsy of lungskos:closeMatchNCIT:C51748Lung Biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymoio:hasExactSynonymlung biopsy
31MAXO:0000381biopsy of lymph nodeskos:closeMatchNCIT:C51900Lymph Node Biopsysemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of lymph node
32MAXO:0000381biopsy of lymph nodeskos:closeMatchNCIT:C51900Lymph Node Biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymrdfs:labellymph node biopsy
33MAXO:0000381biopsy of lymph nodeskos:closeMatchNCIT:C51900Lymph Node Biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymoio:hasExactSynonymlymph node biopsy
34MAXO:0000385biopsy of mouthskos:closeMatchNCIT:C51895Muscle Biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymoio:hasExactSynonymmuscle biopsy
35MAXO:0000385biopsy of mouthskos:closeMatchNCIT:C51895Muscle Biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymrdfs:labelmuscle biopsy
36MAXO:0000385biopsy of mouthskos:closeMatchNCIT:C51650Biopsy of Mouthsemapv:LexicalMatchingoaklib0.5rdfs:labelrdfs:labelbiopsy of mouth
37MAXO:0000385biopsy of mouthskos:closeMatchNCIT:C51650Biopsy of Mouthsemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of mouth
38MAXO:0000386biopsy of muscleskos:closeMatchNCIT:C51895Muscle Biopsysemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of muscle
39MAXO:0000389biopsy of nasopharynxskos:closeMatchNCIT:C51768Biopsy of Nasopharynxsemapv:LexicalMatchingoaklib0.5rdfs:labelrdfs:labelbiopsy of nasopharynx
40MAXO:0000389biopsy of nasopharynxskos:closeMatchNCIT:C51768Biopsy of Nasopharynxsemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of nasopharynx
41MAXO:0000392biopsy of pancreasskos:closeMatchNCIT:C51671Biopsy of Pancreassemapv:LexicalMatchingoaklib0.5rdfs:labelrdfs:labelbiopsy of pancreas
42MAXO:0000392biopsy of pancreasskos:closeMatchNCIT:C51671Biopsy of Pancreassemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of pancreas
43MAXO:0000395biopsy of peritoneumskos:closeMatchNCIT:C51627Biopsy of Peritoneumsemapv:LexicalMatchingoaklib0.5rdfs:labelrdfs:labelbiopsy of peritoneum
44MAXO:0000395biopsy of peritoneumskos:closeMatchNCIT:C51627Biopsy of Peritoneumsemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of peritoneum
45MAXO:0000397biopsy of pleuraskos:closeMatchNCIT:C51897Pleural Biopsysemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of pleura
46MAXO:0000398biopsy of rectumskos:closeMatchNCIT:C51693Rectal Biopsysemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of rectum
47MAXO:0000403biopsy of small intestineskos:closeMatchNCIT:C51600Biopsy of Small Intestinesemapv:LexicalMatchingoaklib0.5rdfs:labelrdfs:labelbiopsy of small intestine
48MAXO:0000403biopsy of small intestineskos:closeMatchNCIT:C51600Biopsy of Small Intestinesemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of small intestine
49MAXO:0000406biopsy of stomachskos:closeMatchNCIT:C51685Gastric Biopsysemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of stomach
50MAXO:0000409biopsy of testisskos:closeMatchNCIT:C51894Biopsy of Testissemapv:LexicalMatchingoaklib0.5rdfs:labelrdfs:labelbiopsy of testis
51MAXO:0000409biopsy of testisskos:closeMatchNCIT:C51894Biopsy of Testissemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of testis
52MAXO:0000411biopsy of thyroid glandskos:closeMatchNCIT:C51613Biopsy of Thyroid Glandsemapv:LexicalMatchingoaklib0.5rdfs:labelrdfs:labelbiopsy of thyroid gland
53MAXO:0000411biopsy of thyroid glandskos:closeMatchNCIT:C51613Biopsy of Thyroid Glandsemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of thyroid gland
54MAXO:0000412biopsy of tongueskos:closeMatchNCIT:C51930Biopsy of Tonguesemapv:LexicalMatchingoaklib0.5rdfs:labelrdfs:labelbiopsy of tongue
55MAXO:0000412biopsy of tongueskos:closeMatchNCIT:C51930Biopsy of Tonguesemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of tongue
56MAXO:0000414biopsy of tracheaskos:closeMatchNCIT:C51631Biopsy of Tracheasemapv:LexicalMatchingoaklib0.5rdfs:labelrdfs:labelbiopsy of trachea
57MAXO:0000414biopsy of tracheaskos:closeMatchNCIT:C51631Biopsy of Tracheasemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of trachea
58MAXO:0000418biopsy of urethraskos:closeMatchNCIT:C51640Biopsy of Urethrasemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of urethra
59MAXO:0000418biopsy of urethraskos:closeMatchNCIT:C51640Biopsy of Urethrasemapv:LexicalMatchingoaklib0.5rdfs:labelrdfs:labelbiopsy of urethra
60MAXO:0000423biopsy of skinskos:closeMatchNCIT:C51692Skin Biopsysemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of skin
61MAXO:0000423biopsy of skinskos:closeMatchNCIT:C51692Skin Biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymrdfs:labelskin biopsy
62MAXO:0000423biopsy of skinskos:closeMatchNCIT:C51692Skin Biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymoio:hasExactSynonymskin biopsy
63MAXO:0000755liquid biopsyskos:closeMatchNCIT:C135727Liquid Biopsysemapv:LexicalMatchingoaklib0.5rdfs:labelrdfs:labelliquid biopsy
64MAXO:0000755liquid biopsyskos:closeMatchNCIT:C135727Liquid Biopsysemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymliquid biopsy
65MAXO:0001121biopsy of kidneyskos:closeMatchNCIT:C51699Kidney Biopsysemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymbiopsy of kidney
66MAXO:0001121biopsy of kidneyskos:closeMatchNCIT:C51699Kidney Biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymrdfs:labelkidney biopsy
67MAXO:0001121biopsy of kidneyskos:closeMatchNCIT:C51699Kidney Biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymoio:hasExactSynonymkidney biopsy
68NCIT:C137909Computed Tomography Assisted Biopsyskos:closeMatchOBI:0002652computed tomography assisted biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymrdfs:labelcomputed tomography assisted biopsy
69NCIT:C137909Computed Tomography Assisted Biopsyskos:closeMatchOBI:0002652computed tomography assisted biopsysemapv:LexicalMatchingoaklib0.5rdfs:labelrdfs:labelcomputed tomography assisted biopsy
70NCIT:C15189Biopsyskos:closeMatchOBI:0002650biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymrdfs:labelbiopsy
71NCIT:C15189Biopsyskos:closeMatchOBI:0002650biopsysemapv:LexicalMatchingoaklib0.5rdfs:labelrdfs:labelbiopsy
72NCIT:C15189Biopsyskos:closeMatchOBI:0002650biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymrdfs:labelbiopsy
73NCIT:C15189Biopsyskos:closeMatchOBI:0002650biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymrdfs:labelbiopsy
74NCIT:C15190Needle Biopsyskos:closeMatchNCIT:C15680Core Biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymoio:hasExactSynonymneedle biopsy
75NCIT:C15190Needle Biopsyskos:closeMatchOBI:0002654needle biopsysemapv:LexicalMatchingoaklib0.5rdfs:labelrdfs:labelneedle biopsy
76NCIT:C15190Needle Biopsyskos:closeMatchOBI:0002654needle biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymrdfs:labelneedle biopsy
77NCIT:C15190Needle Biopsyskos:closeMatchOBI:0002654needle biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymrdfs:labelneedle biopsy
78NCIT:C15190Needle Biopsyskos:closeMatchNCIT:C15680Core Biopsysemapv:LexicalMatchingoaklib0.5rdfs:labeloio:hasExactSynonymneedle biopsy
79NCIT:C15190Needle Biopsyskos:closeMatchNCIT:C15680Core Biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymoio:hasExactSynonymneedle biopsy
80NCIT:C15385Excisional Biopsyskos:closeMatchOBI:0002657surgical biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymrdfs:labelsurgical biopsy
81NCIT:C15652Image Guided Biopsyskos:closeMatchOBI:0002651image guided biopsysemapv:LexicalMatchingoaklib0.5rdfs:labelrdfs:labelimage guided biopsy
82NCIT:C15652Image Guided Biopsyskos:closeMatchOBI:0002651image guided biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymrdfs:labelimage guided biopsy
83NCIT:C15680Core Biopsyskos:closeMatchOBI:0002654needle biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymrdfs:labelneedle biopsy
84NCIT:C15680Core Biopsyskos:closeMatchOBI:0002656core needle biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymrdfs:labelcore needle biopsy
85NCIT:C15680Core Biopsyskos:closeMatchOBI:0002656core needle biopsysemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymrdfs:labelcore needle biopsy
86NCIT:C174241EWS Biopsy/Surgical Procedures Tableskos:closeMatchNCIT:C177402GCT Biopsy/Surgical Procedures Tablesemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymoio:hasExactSynonymbiopsy/surgical procedures table
87NCIT:C174241EWS Biopsy/Surgical Procedures Tableskos:closeMatchNCIT:C179482OS Biopsy/Surgical Procedures Tablesemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymoio:hasExactSynonymbiopsy/surgical procedures table
88NCIT:C174241EWS Biopsy/Surgical Procedures Tableskos:closeMatchNCIT:C186321HL Biopsy/Surgical Procedures Tablesemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymoio:hasExactSynonymbiopsy/surgical procedures table
89NCIT:C177402GCT Biopsy/Surgical Procedures Tableskos:closeMatchNCIT:C179482OS Biopsy/Surgical Procedures Tablesemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymoio:hasExactSynonymbiopsy/surgical procedures table
90NCIT:C177402GCT Biopsy/Surgical Procedures Tableskos:closeMatchNCIT:C186321HL Biopsy/Surgical Procedures Tablesemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymoio:hasExactSynonymbiopsy/surgical procedures table
91NCIT:C179482OS Biopsy/Surgical Procedures Tableskos:closeMatchNCIT:C186321HL Biopsy/Surgical Procedures Tablesemapv:LexicalMatchingoaklib0.5oio:hasExactSynonymoio:hasExactSynonymbiopsy/surgical procedures table
\n", "
" ], "text/plain": [ " subject_id subject_label predicate_id \\\n", "0 MAXO:0000332 biopsy of anus skos:closeMatch \n", "1 MAXO:0000332 biopsy of anus skos:closeMatch \n", "2 MAXO:0000336 biopsy of bone marrow skos:closeMatch \n", "3 MAXO:0000336 biopsy of bone marrow skos:closeMatch \n", "4 MAXO:0000336 biopsy of bone marrow skos:closeMatch \n", "5 MAXO:0000336 biopsy of bone marrow skos:closeMatch \n", "6 MAXO:0000338 biopsy of brain skos:closeMatch \n", "7 MAXO:0000338 biopsy of brain skos:closeMatch \n", "8 MAXO:0000338 biopsy of brain skos:closeMatch \n", "9 MAXO:0000340 biopsy of breast skos:closeMatch \n", "10 MAXO:0000340 biopsy of breast skos:closeMatch \n", "11 MAXO:0000340 biopsy of breast skos:closeMatch \n", "12 MAXO:0000341 biopsy of bronchus skos:closeMatch \n", "13 MAXO:0000350 biopsy of colon skos:closeMatch \n", "14 MAXO:0000350 biopsy of colon skos:closeMatch \n", "15 MAXO:0000355 biopsy of duodenum skos:closeMatch \n", "16 MAXO:0000355 biopsy of duodenum skos:closeMatch \n", "17 MAXO:0000359 biopsy of esophagus skos:closeMatch \n", "18 MAXO:0000366 biopsy of heart skos:closeMatch \n", "19 MAXO:0000366 biopsy of heart skos:closeMatch \n", "20 MAXO:0000373 biopsy of larynx skos:closeMatch \n", "21 MAXO:0000373 biopsy of larynx skos:closeMatch \n", "22 MAXO:0000375 biopsy of lip skos:closeMatch \n", "23 MAXO:0000375 biopsy of lip skos:closeMatch \n", "24 MAXO:0000376 biopsy of liver skos:closeMatch \n", "25 MAXO:0000376 biopsy of liver skos:closeMatch \n", "26 MAXO:0000376 biopsy of liver skos:closeMatch \n", "27 MAXO:0000380 biopsy of lung skos:closeMatch \n", "28 MAXO:0000380 biopsy of lung skos:closeMatch \n", "29 MAXO:0000380 biopsy of lung skos:closeMatch \n", "30 MAXO:0000380 biopsy of lung skos:closeMatch \n", "31 MAXO:0000381 biopsy of lymph node skos:closeMatch \n", "32 MAXO:0000381 biopsy of lymph node skos:closeMatch \n", "33 MAXO:0000381 biopsy of lymph node skos:closeMatch \n", "34 MAXO:0000385 biopsy of mouth skos:closeMatch \n", "35 MAXO:0000385 biopsy of mouth skos:closeMatch \n", "36 MAXO:0000385 biopsy of mouth skos:closeMatch \n", "37 MAXO:0000385 biopsy of mouth skos:closeMatch \n", "38 MAXO:0000386 biopsy of muscle skos:closeMatch \n", "39 MAXO:0000389 biopsy of nasopharynx skos:closeMatch \n", "40 MAXO:0000389 biopsy of nasopharynx skos:closeMatch \n", "41 MAXO:0000392 biopsy of pancreas skos:closeMatch \n", "42 MAXO:0000392 biopsy of pancreas skos:closeMatch \n", "43 MAXO:0000395 biopsy of peritoneum skos:closeMatch \n", "44 MAXO:0000395 biopsy of peritoneum skos:closeMatch \n", "45 MAXO:0000397 biopsy of pleura skos:closeMatch \n", "46 MAXO:0000398 biopsy of rectum skos:closeMatch \n", "47 MAXO:0000403 biopsy of small intestine skos:closeMatch \n", "48 MAXO:0000403 biopsy of small intestine skos:closeMatch \n", "49 MAXO:0000406 biopsy of stomach skos:closeMatch \n", "50 MAXO:0000409 biopsy of testis skos:closeMatch \n", "51 MAXO:0000409 biopsy of testis skos:closeMatch \n", "52 MAXO:0000411 biopsy of thyroid gland skos:closeMatch \n", "53 MAXO:0000411 biopsy of thyroid gland skos:closeMatch \n", "54 MAXO:0000412 biopsy of tongue skos:closeMatch \n", "55 MAXO:0000412 biopsy of tongue skos:closeMatch \n", "56 MAXO:0000414 biopsy of trachea skos:closeMatch \n", "57 MAXO:0000414 biopsy of trachea skos:closeMatch \n", "58 MAXO:0000418 biopsy of urethra skos:closeMatch \n", "59 MAXO:0000418 biopsy of urethra skos:closeMatch \n", "60 MAXO:0000423 biopsy of skin skos:closeMatch \n", "61 MAXO:0000423 biopsy of skin skos:closeMatch \n", "62 MAXO:0000423 biopsy of skin skos:closeMatch \n", "63 MAXO:0000755 liquid biopsy skos:closeMatch \n", "64 MAXO:0000755 liquid biopsy skos:closeMatch \n", "65 MAXO:0001121 biopsy of kidney skos:closeMatch \n", "66 MAXO:0001121 biopsy of kidney skos:closeMatch \n", "67 MAXO:0001121 biopsy of kidney skos:closeMatch \n", "68 NCIT:C137909 Computed Tomography Assisted Biopsy skos:closeMatch \n", "69 NCIT:C137909 Computed Tomography Assisted Biopsy skos:closeMatch \n", "70 NCIT:C15189 Biopsy skos:closeMatch \n", "71 NCIT:C15189 Biopsy skos:closeMatch \n", "72 NCIT:C15189 Biopsy skos:closeMatch \n", "73 NCIT:C15189 Biopsy skos:closeMatch \n", "74 NCIT:C15190 Needle Biopsy skos:closeMatch \n", "75 NCIT:C15190 Needle Biopsy skos:closeMatch \n", "76 NCIT:C15190 Needle Biopsy skos:closeMatch \n", "77 NCIT:C15190 Needle Biopsy skos:closeMatch \n", "78 NCIT:C15190 Needle Biopsy skos:closeMatch \n", "79 NCIT:C15190 Needle Biopsy skos:closeMatch \n", "80 NCIT:C15385 Excisional Biopsy skos:closeMatch \n", "81 NCIT:C15652 Image Guided Biopsy skos:closeMatch \n", "82 NCIT:C15652 Image Guided Biopsy skos:closeMatch \n", "83 NCIT:C15680 Core Biopsy skos:closeMatch \n", "84 NCIT:C15680 Core Biopsy skos:closeMatch \n", "85 NCIT:C15680 Core Biopsy skos:closeMatch \n", "86 NCIT:C174241 EWS Biopsy/Surgical Procedures Table skos:closeMatch \n", "87 NCIT:C174241 EWS Biopsy/Surgical Procedures Table skos:closeMatch \n", "88 NCIT:C174241 EWS Biopsy/Surgical Procedures Table skos:closeMatch \n", "89 NCIT:C177402 GCT Biopsy/Surgical Procedures Table skos:closeMatch \n", "90 NCIT:C177402 GCT Biopsy/Surgical Procedures Table skos:closeMatch \n", "91 NCIT:C179482 OS Biopsy/Surgical Procedures Table skos:closeMatch \n", "\n", " object_id object_label \\\n", "0 NCIT:C51586 Biopsy of Anus \n", "1 NCIT:C51586 Biopsy of Anus \n", "2 NCIT:C15193 Bone Marrow Biopsy \n", "3 NCIT:C15193 Bone Marrow Biopsy \n", "4 NCIT:C15193 Bone Marrow Biopsy \n", "5 NCIT:C15193 Bone Marrow Biopsy \n", "6 NCIT:C51766 Biopsy of Brain \n", "7 NCIT:C51766 Biopsy of Brain \n", "8 NCIT:C51766 Biopsy of Brain \n", "9 NCIT:C51698 Biopsy of Breast \n", "10 NCIT:C51698 Biopsy of Breast \n", "11 NCIT:C51698 Biopsy of Breast \n", "12 NCIT:C51782 Bronchial Biopsy \n", "13 NCIT:C51678 Biopsy of Colon \n", "14 NCIT:C51678 Biopsy of Colon \n", "15 NCIT:C51683 Biopsy of Duodenum \n", "16 NCIT:C51683 Biopsy of Duodenum \n", "17 NCIT:C51686 Esophageal Biopsy \n", "18 NCIT:C51794 Biopsy of Heart \n", "19 NCIT:C51794 Biopsy of Heart \n", "20 NCIT:C51663 Biopsy of Larynx \n", "21 NCIT:C51663 Biopsy of Larynx \n", "22 NCIT:C51653 Biopsy of Lip \n", "23 NCIT:C51653 Biopsy of Lip \n", "24 NCIT:C51677 Liver Biopsy \n", "25 NCIT:C51677 Liver Biopsy \n", "26 NCIT:C51677 Liver Biopsy \n", "27 NCIT:C51748 Lung Biopsy \n", "28 NCIT:C51748 Lung Biopsy \n", "29 NCIT:C51748 Lung Biopsy \n", "30 NCIT:C51748 Lung Biopsy \n", "31 NCIT:C51900 Lymph Node Biopsy \n", "32 NCIT:C51900 Lymph Node Biopsy \n", "33 NCIT:C51900 Lymph Node Biopsy \n", "34 NCIT:C51895 Muscle Biopsy \n", "35 NCIT:C51895 Muscle Biopsy \n", "36 NCIT:C51650 Biopsy of Mouth \n", "37 NCIT:C51650 Biopsy of Mouth \n", "38 NCIT:C51895 Muscle Biopsy \n", "39 NCIT:C51768 Biopsy of Nasopharynx \n", "40 NCIT:C51768 Biopsy of Nasopharynx \n", "41 NCIT:C51671 Biopsy of Pancreas \n", "42 NCIT:C51671 Biopsy of Pancreas \n", "43 NCIT:C51627 Biopsy of Peritoneum \n", "44 NCIT:C51627 Biopsy of Peritoneum \n", "45 NCIT:C51897 Pleural Biopsy \n", "46 NCIT:C51693 Rectal Biopsy \n", "47 NCIT:C51600 Biopsy of Small Intestine \n", "48 NCIT:C51600 Biopsy of Small Intestine \n", "49 NCIT:C51685 Gastric Biopsy \n", "50 NCIT:C51894 Biopsy of Testis \n", "51 NCIT:C51894 Biopsy of Testis \n", "52 NCIT:C51613 Biopsy of Thyroid Gland \n", "53 NCIT:C51613 Biopsy of Thyroid Gland \n", "54 NCIT:C51930 Biopsy of Tongue \n", "55 NCIT:C51930 Biopsy of Tongue \n", "56 NCIT:C51631 Biopsy of Trachea \n", "57 NCIT:C51631 Biopsy of Trachea \n", "58 NCIT:C51640 Biopsy of Urethra \n", "59 NCIT:C51640 Biopsy of Urethra \n", "60 NCIT:C51692 Skin Biopsy \n", "61 NCIT:C51692 Skin Biopsy \n", "62 NCIT:C51692 Skin Biopsy \n", "63 NCIT:C135727 Liquid Biopsy \n", "64 NCIT:C135727 Liquid Biopsy \n", "65 NCIT:C51699 Kidney Biopsy \n", "66 NCIT:C51699 Kidney Biopsy \n", "67 NCIT:C51699 Kidney Biopsy \n", "68 OBI:0002652 computed tomography assisted biopsy \n", "69 OBI:0002652 computed tomography assisted biopsy \n", "70 OBI:0002650 biopsy \n", "71 OBI:0002650 biopsy \n", "72 OBI:0002650 biopsy \n", "73 OBI:0002650 biopsy \n", "74 NCIT:C15680 Core Biopsy \n", "75 OBI:0002654 needle biopsy \n", "76 OBI:0002654 needle biopsy \n", "77 OBI:0002654 needle biopsy \n", "78 NCIT:C15680 Core Biopsy \n", "79 NCIT:C15680 Core Biopsy \n", "80 OBI:0002657 surgical biopsy \n", "81 OBI:0002651 image guided biopsy \n", "82 OBI:0002651 image guided biopsy \n", "83 OBI:0002654 needle biopsy \n", "84 OBI:0002656 core needle biopsy \n", "85 OBI:0002656 core needle biopsy \n", "86 NCIT:C177402 GCT Biopsy/Surgical Procedures Table \n", "87 NCIT:C179482 OS Biopsy/Surgical Procedures Table \n", "88 NCIT:C186321 HL Biopsy/Surgical Procedures Table \n", "89 NCIT:C179482 OS Biopsy/Surgical Procedures Table \n", "90 NCIT:C186321 HL Biopsy/Surgical Procedures Table \n", "91 NCIT:C186321 HL Biopsy/Surgical Procedures Table \n", "\n", " mapping_justification mapping_tool confidence subject_match_field \\\n", "0 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "1 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "2 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "3 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "4 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "5 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "6 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "7 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "8 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "9 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "10 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "11 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "12 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "13 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "14 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "15 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "16 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "17 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "18 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "19 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "20 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "21 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "22 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "23 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "24 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "25 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "26 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "27 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "28 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "29 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "30 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "31 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "32 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "33 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "34 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "35 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "36 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "37 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "38 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "39 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "40 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "41 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "42 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "43 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "44 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "45 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "46 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "47 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "48 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "49 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "50 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "51 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "52 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "53 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "54 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "55 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "56 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "57 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "58 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "59 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "60 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "61 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "62 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "63 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "64 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "65 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "66 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "67 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "68 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "69 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "70 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "71 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "72 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "73 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "74 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "75 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "76 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "77 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "78 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "79 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "80 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "81 semapv:LexicalMatching oaklib 0.5 rdfs:label \n", "82 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "83 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "84 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "85 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "86 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "87 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "88 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "89 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "90 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "91 semapv:LexicalMatching oaklib 0.5 oio:hasExactSynonym \n", "\n", " object_match_field match_string \n", "0 rdfs:label biopsy of anus \n", "1 oio:hasExactSynonym biopsy of anus \n", "2 oio:hasExactSynonym biopsy of bone marrow \n", "3 rdfs:label bone marrow biopsy \n", "4 oio:hasExactSynonym bone marrow biopsy \n", "5 oio:hasExactSynonym bone marrow biopsy \n", "6 rdfs:label biopsy of brain \n", "7 oio:hasExactSynonym biopsy of brain \n", "8 oio:hasExactSynonym brain biopsy \n", "9 oio:hasExactSynonym biopsy of breast \n", "10 oio:hasExactSynonym breast biopsy \n", "11 rdfs:label biopsy of breast \n", "12 oio:hasExactSynonym biopsy of bronchus \n", "13 rdfs:label biopsy of colon \n", "14 oio:hasExactSynonym biopsy of colon \n", "15 rdfs:label biopsy of duodenum \n", "16 oio:hasExactSynonym biopsy of duodenum \n", "17 oio:hasExactSynonym biopsy of esophagus \n", "18 rdfs:label biopsy of heart \n", "19 oio:hasExactSynonym biopsy of heart \n", "20 oio:hasExactSynonym biopsy of larynx \n", "21 rdfs:label biopsy of larynx \n", "22 oio:hasExactSynonym biopsy of lip \n", "23 rdfs:label biopsy of lip \n", "24 oio:hasExactSynonym biopsy of liver \n", "25 rdfs:label liver biopsy \n", "26 oio:hasExactSynonym liver biopsy \n", "27 oio:hasExactSynonym biopsy of lung \n", "28 rdfs:label lung biopsy \n", "29 oio:hasExactSynonym lung biopsy \n", "30 oio:hasExactSynonym lung biopsy \n", "31 oio:hasExactSynonym biopsy of lymph node \n", "32 rdfs:label lymph node biopsy \n", "33 oio:hasExactSynonym lymph node biopsy \n", "34 oio:hasExactSynonym muscle biopsy \n", "35 rdfs:label muscle biopsy \n", "36 rdfs:label biopsy of mouth \n", "37 oio:hasExactSynonym biopsy of mouth \n", "38 oio:hasExactSynonym biopsy of muscle \n", "39 rdfs:label biopsy of nasopharynx \n", "40 oio:hasExactSynonym biopsy of nasopharynx \n", "41 rdfs:label biopsy of pancreas \n", "42 oio:hasExactSynonym biopsy of pancreas \n", "43 rdfs:label biopsy of peritoneum \n", "44 oio:hasExactSynonym biopsy of peritoneum \n", "45 oio:hasExactSynonym biopsy of pleura \n", "46 oio:hasExactSynonym biopsy of rectum \n", "47 rdfs:label biopsy of small intestine \n", "48 oio:hasExactSynonym biopsy of small intestine \n", "49 oio:hasExactSynonym biopsy of stomach \n", "50 rdfs:label biopsy of testis \n", "51 oio:hasExactSynonym biopsy of testis \n", "52 rdfs:label biopsy of thyroid gland \n", "53 oio:hasExactSynonym biopsy of thyroid gland \n", "54 rdfs:label biopsy of tongue \n", "55 oio:hasExactSynonym biopsy of tongue \n", "56 rdfs:label biopsy of trachea \n", "57 oio:hasExactSynonym biopsy of trachea \n", "58 oio:hasExactSynonym biopsy of urethra \n", "59 rdfs:label biopsy of urethra \n", "60 oio:hasExactSynonym biopsy of skin \n", "61 rdfs:label skin biopsy \n", "62 oio:hasExactSynonym skin biopsy \n", "63 rdfs:label liquid biopsy \n", "64 oio:hasExactSynonym liquid biopsy \n", "65 oio:hasExactSynonym biopsy of kidney \n", "66 rdfs:label kidney biopsy \n", "67 oio:hasExactSynonym kidney biopsy \n", "68 rdfs:label computed tomography assisted biopsy \n", "69 rdfs:label computed tomography assisted biopsy \n", "70 rdfs:label biopsy \n", "71 rdfs:label biopsy \n", "72 rdfs:label biopsy \n", "73 rdfs:label biopsy \n", "74 oio:hasExactSynonym needle biopsy \n", "75 rdfs:label needle biopsy \n", "76 rdfs:label needle biopsy \n", "77 rdfs:label needle biopsy \n", "78 oio:hasExactSynonym needle biopsy \n", "79 oio:hasExactSynonym needle biopsy \n", "80 rdfs:label surgical biopsy \n", "81 rdfs:label image guided biopsy \n", "82 rdfs:label image guided biopsy \n", "83 rdfs:label needle biopsy \n", "84 rdfs:label core needle biopsy \n", "85 rdfs:label core needle biopsy \n", "86 oio:hasExactSynonym biopsy/surgical procedures table \n", "87 oio:hasExactSynonym biopsy/surgical procedures table \n", "88 oio:hasExactSynonym biopsy/surgical procedures table \n", "89 oio:hasExactSynonym biopsy/surgical procedures table \n", "90 oio:hasExactSynonym biopsy/surgical procedures table \n", "91 oio:hasExactSynonym biopsy/surgical procedures table " ] }, "execution_count": 45, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df = pd.read_csv(\"output/maxo-lexmatch-ncit-biopsy.sssom.tsv\", sep=\"\\t\", comment=\"#\").fillna(\"\")\n", "df" ] }, { "cell_type": "code", "execution_count": null, "id": "46103ec9", "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.9.5" } }, "nbformat": 4, "nbformat_minor": 5 }