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Added additional documentation to why-predicates notebook #332

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Added additional documentation to why-predicates notebook #332

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8438892
Monarch tutorial for tomorrow
cmungall Oct 25, 2022
2134cf7
ignoring B027 (why did this start now?)
cmungall Oct 25, 2022
c5cfa6e
Adding info
cmungall Oct 25, 2022
4253ccb
Merge branch 'main' into why-predicates-lesson
cmungall Jan 20, 2024
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131 changes: 79 additions & 52 deletions notebooks/Lessons/Why-predicates-are-important.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,14 @@
"\n",
"This notebook is intended as an explanatory guide to the importance of edge types (predicates) in ontologies.\n",
"\n",
"Lessons:\n",
"\n",
"- using OAK and the sqlite backend\n",
"- understand the structure of key acids in CHEBI\n",
"- learn how paramaterizing by predicates makes a difference to measures like semantic similarity\n",
"- learm how to \"debug\" using OAK viz\n",
"- understand what Relation Graph is and why it's important\n",
"\n",
"## Citric acid and its ion forms\n",
"\n",
"For this guide, we are going to look at citric acid and it's conjugate forms such as citrate(3-). These\n",
Expand Down Expand Up @@ -76,7 +84,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 2,
"id": "f6468023",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -105,7 +113,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 3,
"id": "a54bf0e2",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -195,51 +203,51 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 4,
"id": "ebf64216",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"IAO:0000115: A tricarboxylic acid trianion, obtained by deprotonation of the three\r\n",
" carboxy groups of citric acid.\r\n",
"id: CHEBI:16947\r\n",
"obo:chebi/charge: '-3'\r\n",
"obo:chebi/formula: C6H5O7\r\n",
"obo:chebi/inchi: InChI=1S/C6H8O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12)/p-3\r\n",
"obo:chebi/inchikey: KRKNYBCHXYNGOX-UHFFFAOYSA-K\r\n",
"obo:chebi/mass: '189.09970'\r\n",
"obo:chebi/monoisotopicmass: '189.00517'\r\n",
"obo:chebi/smiles: OC(CC([O-])=O)(CC([O-])=O)C([O-])=O\r\n",
"oio:hasAlternativeId:\r\n",
"- CHEBI:13999\r\n",
"- CHEBI:23321\r\n",
"- CHEBI:42563\r\n",
"oio:hasDbXref:\r\n",
"- Beilstein:1884707\r\n",
"- CAS:126-44-3\r\n",
"- Gmelin:4239\r\n",
"- KEGG:C00158\r\n",
"- PDBeChem:FLC\r\n",
"- Reaxys:1884707\r\n",
"oio:hasExactSynonym: 2-hydroxypropane-1,2,3-tricarboxylate\r\n",
"oio:hasOBONamespace: chebi_ontology\r\n",
"oio:hasRelatedSynonym:\r\n",
"- 2-hydroxy-1,2,3-propanetricarboxylate\r\n",
"- 2-hydroxy-1,2,3-propanetricarboxylate(3-)\r\n",
"- 2-hydroxy-1,2,3-propanetricarboxylic acid, ion(3-)\r\n",
"- 2-hydroxytricarballylate\r\n",
"- CITRATE ANION\r\n",
"- cit\r\n",
"- cit(3-)\r\n",
"- citrate\r\n",
"oio:id: CHEBI:16947\r\n",
"oio:inSubset: obo:chebi#3_STAR\r\n",
"rdfs:label: citrate(3-)\r\n",
"\r\n",
"---\r\n"
"IAO:0000115: A tricarboxylic acid trianion, obtained by deprotonation of the three\n",
" carboxy groups of citric acid.\n",
"id: CHEBI:16947\n",
"obo:chebi/charge: '-3'\n",
"obo:chebi/formula: C6H5O7\n",
"obo:chebi/inchi: InChI=1S/C6H8O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12)/p-3\n",
"obo:chebi/inchikey: KRKNYBCHXYNGOX-UHFFFAOYSA-K\n",
"obo:chebi/mass: '189.09970'\n",
"obo:chebi/monoisotopicmass: '189.00517'\n",
"obo:chebi/smiles: OC(CC([O-])=O)(CC([O-])=O)C([O-])=O\n",
"oio:hasAlternativeId:\n",
"- CHEBI:13999\n",
"- CHEBI:23321\n",
"- CHEBI:42563\n",
"oio:hasDbXref:\n",
"- Beilstein:1884707\n",
"- CAS:126-44-3\n",
"- Gmelin:4239\n",
"- KEGG:C00158\n",
"- PDBeChem:FLC\n",
"- Reaxys:1884707\n",
"oio:hasExactSynonym: 2-hydroxypropane-1,2,3-tricarboxylate\n",
"oio:hasOBONamespace: chebi_ontology\n",
"oio:hasRelatedSynonym:\n",
"- 2-hydroxy-1,2,3-propanetricarboxylate\n",
"- 2-hydroxy-1,2,3-propanetricarboxylate(3-)\n",
"- 2-hydroxy-1,2,3-propanetricarboxylic acid, ion(3-)\n",
"- 2-hydroxytricarballylate\n",
"- CITRATE ANION\n",
"- cit\n",
"- cit(3-)\n",
"- citrate\n",
"oio:id: CHEBI:16947\n",
"oio:inSubset: obo:chebi#3_STAR\n",
"rdfs:label: citrate(3-)\n",
"\n",
"---\n"
]
}
],
Expand Down Expand Up @@ -593,7 +601,7 @@
},
{
"cell_type": "code",
"execution_count": 15,
"execution_count": 5,
"id": "c253b1eb",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -654,7 +662,7 @@
},
{
"cell_type": "code",
"execution_count": 17,
"execution_count": 6,
"id": "b25f97fe",
"metadata": {},
"outputs": [],
Expand All @@ -675,7 +683,7 @@
},
{
"cell_type": "code",
"execution_count": 24,
"execution_count": 7,
"id": "c6394e2d",
"metadata": {},
"outputs": [],
Expand All @@ -693,7 +701,7 @@
},
{
"cell_type": "code",
"execution_count": 26,
"execution_count": 8,
"id": "b8a665d6",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -861,7 +869,7 @@
"[304 rows x 6 columns]"
]
},
"execution_count": 26,
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
Expand Down Expand Up @@ -897,24 +905,43 @@
},
{
"cell_type": "code",
"execution_count": 30,
"execution_count": 10,
"id": "7f9ce93f",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"UBERON:0001612|BFO:0000050|UBERON:0000477\r\n",
"UBERON:0001612|BFO:0000050|UBERON:0010000\r\n",
"UBERON:0001612|BFO:0000050|UBERON:0000055\r\n",
"UBERON:0001612|BFO:0000050|UBERON:0003509\r\n",
"UBERON:0001612|BFO:0000050|UBERON:0001637\r\n"
"CL:0000127|BFO:0000050|UBERON:0000061\r\n",
"CL:0000127|BFO:0000050|UBERON:0000465\r\n",
"CL:0000127|BFO:0000050|UBERON:0000467\r\n",
"CL:0000127|BFO:0000050|UBERON:0000468\r\n",
"CL:0000127|BFO:0000050|UBERON:0001016\r\n"
]
}
],
"source": [
"!echo \"SELECT * FROM entailed_edge WHERE subject='CL:0000127' AND predicate='BFO:0000050' AND object LIKE 'UBERON:%' LIMIT 5\" | sqlite3 $HOME/.data/oaklib/cl.db"
]
},
{
"cell_type": "code",
"execution_count": 11,
"id": "51bac57f",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"UBERON:0000061 ! anatomical structure\r\n",
"UBERON:0001016 ! nervous system\r\n"
]
}
],
"source": [
"!echo \"SELECT * FROM entailed_edge WHERE predicate='BFO:0000050' AND object LIKE 'UBERON:%' LIMIT 5\" | sqlite3 $HOME/.data/oaklib/cl.db"
"cl info UBERON:0000061 UBERON:0001016"
]
},
{
Expand Down