{ "cells": [ { "cell_type": "markdown", "id": "681a0856", "metadata": {}, "source": [ "# OAK diff-via-mappings command\n", "\n", "This notebook is intended as a supplement to the [main OAK CLI docs](https://incatools.github.io/ontology-access-kit/cli.html).\n", "\n", "This notebook provides examples for the `diff-via-mappings` command, which can be used to **find differences between two ontologies based on mappings between them**\n", "\n", "For more on mappings, see [Mappings](https://incatools.github.io/ontology-access-kit/guide/mappings.html) in the OAK guide.\n", "\n", "\n", "## Help Option\n", "\n", "You can get help on any OAK command using `--help`" ] }, { "cell_type": "code", "execution_count": 1, "id": "460639a7", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Usage: runoak diff-via-mappings [OPTIONS] [TERMS]...\r\n", "\r\n", " Calculates cross-ontology diff using mappings\r\n", "\r\n", " Given a pair of ontologies, and mappings that connect terms in both\r\n", " ontologies, this command will perform a structural comparison of all mapped\r\n", " pairs of terms\r\n", "\r\n", " Example:\r\n", "\r\n", " runoak -i sqlite:obo:uberon diff-via-mappings --other-input\r\n", " sqlite:obo:zfa --source UBERON --source ZFA -O csv\r\n", "\r\n", " Note the above command does not have any mapping file specified; the\r\n", " mappings that are distributed within each ontology is used (in this case,\r\n", " Uberon contains mappings to ZFA)\r\n", "\r\n", " If the mappings are provided externally:\r\n", "\r\n", " runoak -i ont1.obo diff-via-mappings --other-input ont2.obo --mapping-\r\n", " input mappings.sssom.tsv\r\n", "\r\n", " (in the above example, --source is not passed, so all mappings are tested)\r\n", "\r\n", " If there are no existing mappings, you can use the lexmatch command to\r\n", " generate them:\r\n", "\r\n", " runoak -i ont1.obo diff-via-mappings -a ont2.obo lexmatch -o\r\n", " mappings.sssom.tsv\r\n", "\r\n", " runoak -i ont1.obo diff-via-mappings --other-input ont2.obo --mapping-\r\n", " input mappings.sssom.tsv\r\n", "\r\n", " The output from this command follows the cross-ontology-diff data model\r\n", " (https://incatools.github.io/ontology-access-kit/datamodels/cross-ontology-\r\n", " diff/index.html)\r\n", "\r\n", " This can be serialized in YAML or TSV form\r\n", "\r\n", "Options:\r\n", " -S, --source TEXT ontology prefixes e.g. HP, MP\r\n", " --mapping-input TEXT File of mappings in SSSOM format. If not\r\n", " provided then mappings in ontology(ies) are\r\n", " used\r\n", " -X, --other-input TEXT Additional input file\r\n", " --other-input-type TEXT Type of additional input file\r\n", " --intra / --no-intra If true, then all sources are in the main\r\n", " input ontology [default: no-intra]\r\n", " --autolabel / --no-autolabel If set, results will automatically have\r\n", " labels assigned [default: autolabel]\r\n", " --include-identity-mappings / --no-include-identity-mappings\r\n", " Use identity relation as mapping; use this\r\n", " for two versions of the same ontology\r\n", " [default: no-include-identity-mappings]\r\n", " --filter-category-identical / --no-filter-category-identical\r\n", " Do not report cases where a relationship has\r\n", " not changed [default: no-filter-category-\r\n", " identical]\r\n", " --bidirectional / --no-bidirectional\r\n", " Show diff from both left and right\r\n", " perspectives [default: bidirectional]\r\n", " -p, --predicates TEXT A comma-separated list of predicates. This\r\n", " may be a shorthand (i, p) or CURIE\r\n", " -o, --output FILENAME Output file, e.g. obo file\r\n", " -O, --output-type TEXT Desired output type\r\n", " --help Show this message and exit.\r\n" ] } ], "source": [ "!runoak diff-via-mappings --help" ] }, { "cell_type": "markdown", "id": "672f0f62", "metadata": {}, "source": [ "## Example: Diff between two anatomy ontologies\n", "\n", "To illustrate usage, we will calculate the diff between [UBERON](https://obofoundry.org/ontology/uberon) (a multi-species anatomy ontology) and [ZFA](https://obofoundry.org/ontology/zfa) (an anatomy ontology for zebrafish).\n", "\n", "Note that rather than provide a set of external mappings, we will use the mappings present in both ontologies (in this case, UBERON has xrefs to ZFA).\n", "\n", "To simplify the comparison, we will only consider [is_a](https://incatools.github.io/ontology-access-kit/glossary.html#term-IS_A) and [part_of](https://incatools.github.io/ontology-access-kit/glossary.html#term-Part-Of) relationships. This is specified using the `--predicates` (`-p`) option" ] }, { "cell_type": "code", "execution_count": 5, "id": "ef4a124b", "metadata": {}, "outputs": [], "source": [ "!runoak -i sqlite:obo:uberon diff-via-mappings --other-input \\\n", " sqlite:obo:zfa --source UBERON --source ZFA -p i,p -O csv -o output/uberon-zfa-diff.csv" ] }, { "cell_type": "markdown", "id": "cb6e5491", "metadata": {}, "source": [ "## Analyzing the results using Pandas\n", "\n", "Note that we asked for the output as a tabular file (`-O csv`), rather than native YAML. You could take the tabular output, analyze it in a spreadsheet, etc. Here we will use the Python pandas library." ] }, { "cell_type": "code", "execution_count": 8, "id": "26c079cc", "metadata": {}, "outputs": [], "source": [ "import pandas as pd\n", "df=pd.read_csv(\"output/uberon-zfa-diff.csv\", sep=\"\\t\").fillna(\"\")" ] }, { "cell_type": "code", "execution_count": 9, "id": "1ad732b4", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | left_subject_id | \n", "left_object_id | \n", "left_predicate_id | \n", "category | \n", "left_subject_label | \n", "left_object_label | \n", "left_predicate_label | \n", "right_subject_id | \n", "right_object_id | \n", "right_predicate_ids | \n", "right_subject_label | \n", "right_object_label | \n", "right_predicate_labels | \n", "left_subject_is_functional | \n", "left_object_is_functional | \n", "subject_mapping_predicate | \n", "object_mapping_predicate | \n", "right_intermediate_ids | \n", "subject_mapping_cardinality | \n", "object_mapping_cardinality | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | \n", "UBERON:0000002 | \n", "UBERON:0000995 | \n", "BFO:0000050 | \n", "MissingMapping | \n", "uterine cervix | \n", "uterus | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | 1:0 | \n", "\n", " |
1 | \n", "UBERON:0000002 | \n", "UBERON:0001560 | \n", "rdfs:subClassOf | \n", "MissingMapping | \n", "uterine cervix | \n", "neck of organ | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | 1:0 | \n", "\n", " |
2 | \n", "UBERON:0000002 | \n", "UBERON:0005156 | \n", "rdfs:subClassOf | \n", "MissingMapping | \n", "uterine cervix | \n", "reproductive structure | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | 1:0 | \n", "\n", " |
3 | \n", "UBERON:0000003 | \n", "UBERON:0000033 | \n", "BFO:0000050 | \n", "MissingMapping | \n", "naris | \n", "head | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | 1:0 | \n", "\n", " |
4 | \n", "UBERON:0000003 | \n", "UBERON:0005725 | \n", "BFO:0000050 | \n", "MissingMapping | \n", "naris | \n", "olfactory system | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | 1:0 | \n", "\n", " |
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
36336 | \n", "ZFA:0009401 | \n", "ZFA:0009000 | \n", "rdfs:subClassOf | \n", "MissingMapping | \n", "lens fiber cell | \n", "cell | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | 1:0 | \n", "\n", " |
36337 | \n", "ZFA:0009402 | \n", "ZFA:0005065 | \n", "BFO:0000050 | \n", "MissingMapping | \n", "heart valve cell | \n", "heart valve | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | 1:0 | \n", "\n", " |
36338 | \n", "ZFA:0009402 | \n", "ZFA:0009000 | \n", "rdfs:subClassOf | \n", "MissingMapping | \n", "heart valve cell | \n", "cell | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | 1:0 | \n", "\n", " |
36339 | \n", "ZFA:0009403 | \n", "ZFA:0009402 | \n", "rdfs:subClassOf | \n", "MissingMapping | \n", "heart valve interstitial cell | \n", "heart valve cell | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | 1:0 | \n", "\n", " |
36340 | \n", "ZFA:0009404 | \n", "ZFA:0009402 | \n", "rdfs:subClassOf | \n", "MissingMapping | \n", "heart valve endothelial cell | \n", "heart valve cell | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | 1:0 | \n", "\n", " |
36341 rows × 20 columns
\n", "\n", " | left_subject_id | \n", "left_object_id | \n", "left_predicate_id | \n", "category | \n", "left_subject_label | \n", "left_object_label | \n", "left_predicate_label | \n", "right_subject_id | \n", "right_object_id | \n", "right_predicate_ids | \n", "right_subject_label | \n", "right_object_label | \n", "right_predicate_labels | \n", "left_subject_is_functional | \n", "left_object_is_functional | \n", "subject_mapping_predicate | \n", "object_mapping_predicate | \n", "right_intermediate_ids | \n", "subject_mapping_cardinality | \n", "object_mapping_cardinality | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
22 | \n", "UBERON:0000010 | \n", "UBERON:0001016 | \n", "BFO:0000050 | \n", "NonEntailedRelationship | \n", "peripheral nervous system | \n", "nervous system | \n", "\n", " | ZFA:0000142 | \n", "ZFA:0000396 | \n", "rdfs:subClassOf | \n", "peripheral nervous system | \n", "nervous system | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
24 | \n", "UBERON:0000011 | \n", "UBERON:0002410 | \n", "BFO:0000050 | \n", "NonEntailedRelationship | \n", "parasympathetic nervous system | \n", "autonomic nervous system | \n", "\n", " | ZFA:0001575 | \n", "ZFA:0001574 | \n", "rdfs:subClassOf | \n", "parasympathetic nervous system | \n", "autonomic nervous system | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
29 | \n", "UBERON:0000013 | \n", "UBERON:0002410 | \n", "BFO:0000050 | \n", "NonEntailedRelationship | \n", "sympathetic nervous system | \n", "autonomic nervous system | \n", "\n", " | ZFA:0001576 | \n", "ZFA:0001574 | \n", "rdfs:subClassOf | \n", "sympathetic nervous system | \n", "autonomic nervous system | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
196 | \n", "UBERON:0000095 | \n", "UBERON:0002342 | \n", "BFO:0000050 | \n", "NonEntailedRelationship | \n", "cardiac neural crest | \n", "neural crest | \n", "\n", " | ZFA:0001648 | \n", "ZFA:0000045 | \n", "rdfs:subClassOf | \n", "cardiac neural crest | \n", "neural crest | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
725 | \n", "UBERON:0000936 | \n", "UBERON:0003931 | \n", "BFO:0000050 | \n", "NonEntailedRelationship | \n", "posterior commissure | \n", "diencephalic white matter | \n", "\n", " | ZFA:0000320 | \n", "ZFA:0000338 | \n", "rdfs:subClassOf | \n", "caudal commissure | \n", "diencephalic white matter | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
35155 | \n", "ZFA:0005661 | \n", "ZFA:0001488 | \n", "rdfs:subClassOf | \n", "NonEntailedRelationship | \n", "olfactory bulb glomerulus | \n", "multi-tissue structure | \n", "\n", " | UBERON:0005387 | \n", "UBERON:0000481 | \n", "BFO:0000050|RO:0002131|RO:0002323 | \n", "olfactory glomerulus | \n", "multi-tissue structure | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
35458 | \n", "ZFA:0005829 | \n", "ZFA:0005249 | \n", "rdfs:subClassOf | \n", "NonEntailedRelationship | \n", "Schlemm's canal | \n", "vasculature | \n", "\n", " | UBERON:0004029 | \n", "UBERON:0002049 | \n", "BFO:0000050|RO:0002131|RO:0002323 | \n", "canal of Schlemm | \n", "vasculature | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
35680 | \n", "ZFA:0007017 | \n", "ZFA:0001477 | \n", "rdfs:subClassOf | \n", "NonEntailedRelationship | \n", "posterior neural plate | \n", "portion of tissue | \n", "\n", " | UBERON:0003057 | \n", "UBERON:0000479 | \n", "BFO:0000050|RO:0002131|RO:0002323 | \n", "chordal neural plate | \n", "tissue | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
35701 | \n", "ZFA:0007037 | \n", "ZFA:0001477 | \n", "rdfs:subClassOf | \n", "NonEntailedRelationship | \n", "posterior neural tube | \n", "portion of tissue | \n", "\n", " | UBERON:0003076 | \n", "UBERON:0000479 | \n", "BFO:0000050|RO:0002131|RO:0002202|RO:0002254|R... | \n", "posterior neural tube | \n", "tissue | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
35702 | \n", "ZFA:0007038 | \n", "ZFA:0001477 | \n", "rdfs:subClassOf | \n", "NonEntailedRelationship | \n", "anterior neural tube | \n", "portion of tissue | \n", "\n", " | UBERON:0003080 | \n", "UBERON:0000479 | \n", "BFO:0000050|RO:0002131|RO:0002202|RO:0002254|R... | \n", "anterior neural tube | \n", "tissue | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
205 rows × 20 columns
\n", "\n", " | left_subject_id | \n", "left_object_id | \n", "left_predicate_id | \n", "category | \n", "left_subject_label | \n", "left_object_label | \n", "left_predicate_label | \n", "right_subject_id | \n", "right_object_id | \n", "right_predicate_ids | \n", "right_subject_label | \n", "right_object_label | \n", "right_predicate_labels | \n", "left_subject_is_functional | \n", "left_object_is_functional | \n", "subject_mapping_predicate | \n", "object_mapping_predicate | \n", "right_intermediate_ids | \n", "subject_mapping_cardinality | \n", "object_mapping_cardinality | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
7 | \n", "UBERON:0000004 | \n", "UBERON:0000475 | \n", "rdfs:subClassOf | \n", "NoRelationship | \n", "nose | \n", "organism subdivision | \n", "\n", " | ZFA:0000047 | \n", "ZFA:0001308 | \n", "\n", " | peripheral olfactory organ | \n", "organism subdivision | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
188 | \n", "UBERON:0000089 | \n", "UBERON:0004750 | \n", "BFO:0000050 | \n", "NoRelationship | \n", "hypoblast (generic) | \n", "blastoderm | \n", "\n", " | ZFA:0000117 | \n", "ZFA:0001176 | \n", "\n", " | hypoblast | \n", "blastoderm | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
647 | \n", "UBERON:0000471 | \n", "UBERON:0003103 | \n", "BFO:0000050 | \n", "NoRelationship | \n", "compound organ component | \n", "compound organ | \n", "\n", " | ZFA:0001489 | \n", "ZFA:0000496 | \n", "\n", " | compound organ component | \n", "compound organ | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
661 | \n", "UBERON:0000479 | \n", "UBERON:0000468 | \n", "BFO:0000050 | \n", "NoRelationship | \n", "tissue | \n", "multicellular organism | \n", "\n", " | ZFA:0001477 | \n", "ZFA:0001094 | \n", "\n", " | portion of tissue | \n", "whole organism | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
663 | \n", "UBERON:0000480 | \n", "UBERON:0000468 | \n", "BFO:0000050 | \n", "NoRelationship | \n", "anatomical group | \n", "multicellular organism | \n", "\n", " | ZFA:0001512 | \n", "ZFA:0001094 | \n", "\n", " | anatomical group | \n", "whole organism | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
35714 | \n", "ZFA:0007057 | \n", "ZFA:0005297 | \n", "rdfs:subClassOf | \n", "NoRelationship | \n", "ocular blood vessel | \n", "cranial blood vessel | \n", "\n", " | UBERON:0002203 | \n", "UBERON:0011362 | \n", "\n", " | vasculature of eye | \n", "cranial blood vasculature | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
35715 | \n", "ZFA:0007058 | \n", "ZFA:0000012 | \n", "BFO:0000050 | \n", "NoRelationship | \n", "roof plate | \n", "central nervous system | \n", "\n", " | UBERON:0003054 | \n", "UBERON:0001017 | \n", "\n", " | roof plate | \n", "central nervous system | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
35716 | \n", "ZFA:0007058 | \n", "ZFA:0001488 | \n", "rdfs:subClassOf | \n", "NoRelationship | \n", "roof plate | \n", "multi-tissue structure | \n", "\n", " | UBERON:0003054 | \n", "UBERON:0000481 | \n", "\n", " | roof plate | \n", "multi-tissue structure | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
35720 | \n", "ZFA:0007071 | \n", "ZFA:0001477 | \n", "rdfs:subClassOf | \n", "NoRelationship | \n", "flexural organ | \n", "portion of tissue | \n", "\n", " | UBERON:0011577 | \n", "UBERON:0000479 | \n", "\n", " | flexural organ | \n", "tissue | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
35722 | \n", "ZFA:0007072 | \n", "ZFA:0001488 | \n", "rdfs:subClassOf | \n", "NoRelationship | \n", "blood sinus | \n", "multi-tissue structure | \n", "\n", " | UBERON:0006615 | \n", "UBERON:0000481 | \n", "\n", " | venous sinus | \n", "multi-tissue structure | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
1375 rows × 20 columns
\n", "\n", " | left_subject_id | \n", "left_object_id | \n", "left_predicate_id | \n", "category | \n", "left_subject_label | \n", "left_object_label | \n", "left_predicate_label | \n", "right_subject_id | \n", "right_object_id | \n", "right_predicate_ids | \n", "... | \n", "right_object_label | \n", "right_predicate_labels | \n", "left_subject_is_functional | \n", "left_object_is_functional | \n", "subject_mapping_predicate | \n", "object_mapping_predicate | \n", "right_intermediate_ids | \n", "subject_mapping_cardinality | \n", "object_mapping_cardinality | \n", "left_source | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
35 | \n", "UBERON:0000016 | \n", "UBERON:0000949 | \n", "BFO:0000050 | \n", "LeftEntailedByRight | \n", "endocrine pancreas | \n", "endocrine system | \n", "\n", " | ZFA:0001260 | \n", "ZFA:0001158 | \n", "BFO:0000050|RO:0002131|RO:0002202 | \n", "... | \n", "endocrine system | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | UBERON | \n", "
91 | \n", "UBERON:0000045 | \n", "UBERON:0001016 | \n", "BFO:0000050 | \n", "LeftEntailedByRight | \n", "ganglion | \n", "nervous system | \n", "\n", " | ZFA:0000190 | \n", "ZFA:0000396 | \n", "BFO:0000050|RO:0002131 | \n", "... | \n", "nervous system | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | UBERON | \n", "
182 | \n", "UBERON:0000086 | \n", "UBERON:0000992 | \n", "BFO:0000050 | \n", "LeftEntailedByRight | \n", "zona pellucida | \n", "ovary | \n", "\n", " | ZFA:0001111 | \n", "ZFA:0000403 | \n", "BFO:0000050|RO:0002131 | \n", "... | \n", "ovary | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | UBERON | \n", "
645 | \n", "UBERON:0000467 | \n", "UBERON:0000061 | \n", "rdfs:subClassOf | \n", "LeftEntailedByRight | \n", "anatomical system | \n", "anatomical structure | \n", "\n", " | ZFA:0001439 | \n", "ZFA:0000037 | \n", "BFO:0000050|RO:0002131|rdfs:subClassOf | \n", "... | \n", "anatomical structure | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | UBERON | \n", "
658 | \n", "UBERON:0000477 | \n", "UBERON:0001062 | \n", "rdfs:subClassOf | \n", "LeftEntailedByRight | \n", "anatomical cluster | \n", "anatomical entity | \n", "\n", " | ZFA:0001478 | \n", "ZFA:0100000 | \n", "rdfs:subClassOf | \n", "... | \n", "zebrafish anatomical entity | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | UBERON | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
35706 | \n", "ZFA:0007043 | \n", "ZFA:0001477 | \n", "rdfs:subClassOf | \n", "LeftEntailedByRight | \n", "hindbrain neural tube | \n", "portion of tissue | \n", "\n", " | UBERON:2007043 | \n", "UBERON:0000479 | \n", "BFO:0000050|RO:0002131|RO:0002202|RO:0002254|R... | \n", "... | \n", "tissue | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | ZFA | \n", "
35711 | \n", "ZFA:0007048 | \n", "ZFA:0005145 | \n", "rdfs:subClassOf | \n", "LeftEntailedByRight | \n", "ventral intermandibularis posterior | \n", "muscle | \n", "\n", " | UBERON:2007048 | \n", "UBERON:0001630 | \n", "RO:0002131|RO:0002202|RO:0002254|RO:0002258|RO... | \n", "... | \n", "muscle organ | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | ZFA | \n", "
35717 | \n", "ZFA:0007068 | \n", "ZFA:0001486 | \n", "rdfs:subClassOf | \n", "LeftEntailedByRight | \n", "otic epithelium | \n", "epithelium | \n", "\n", " | UBERON:0003249 | \n", "UBERON:0000483 | \n", "RO:0002131|RO:0002323|rdfs:subClassOf | \n", "... | \n", "epithelium | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | ZFA | \n", "
35721 | \n", "ZFA:0007072 | \n", "ZFA:0000010 | \n", "BFO:0000050 | \n", "LeftEntailedByRight | \n", "blood sinus | \n", "cardiovascular system | \n", "\n", " | UBERON:0006615 | \n", "UBERON:0004535 | \n", "BFO:0000050|RO:0002131|RO:0002202|RO:0002254|R... | \n", "... | \n", "cardiovascular system | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | ZFA | \n", "
35723 | \n", "ZFA:0007073 | \n", "ZFA:0001643 | \n", "rdfs:subClassOf | \n", "LeftEntailedByRight | \n", "blood sinus cavity | \n", "anatomical space | \n", "\n", " | UBERON:0034940 | \n", "UBERON:0000464 | \n", "rdfs:subClassOf | \n", "... | \n", "anatomical space | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | ZFA | \n", "
883 rows × 21 columns
\n", "