cmungall

{
  "id": "msg_01MUhMFswt344QGvVaDs5Cv4",
  "type": "message",
  "role": "assistant",
  "model": "claude-3-7-sonnet-20250219",
  "content": [
    {
      "type": "text",
      "text": "Let me help fix issue 3003. I'll first check what the issue is about."
    },

cmungall

default_context:
  project_name: natprodkb
  github_org: monarch-initiative
  project_description: Representation of individual natural products and their properties
  attributes: Include the usual metadata (name, description), chemical classification, chemical components, known pathways/genes/gene clusters. Also include details on what plants/species produce them, as well as clinical and other applications.
    Please DO NOT include references or publications in the initial schema, these will be added later. 
  full_name: dragon-ai
  email: [email protected]
  license: BSD-3
  main_schema_class: NaturalProduct

cmungall

change definition of GO:0000008 from 'OBSOLETE. A small disulfide-containing redox protein that serves as a general protein disulfide oxidoreductase. Interacts with a broad range of proteins by a redox mechanism, based on the reversible oxidation of 2 cysteine thiol groups to a disulfide, accompanied by the transfer of 2 electrons and 2 protons. The net result is the covalent interconversion of a disulfide and a dithiol.' to 'OBSOLETE. A small disulfide-containing redox protein that serves as a general protein disulfide oxidoreductase. Interacts with a broad range of proteins by a redox mechanism, based on the reversible oxidation of 2 L-cysteine thiol groups to a disulfide, accompanied by the transfer of 2 electrons and 2 protons. The net result is the covalent interconversion of a disulfide and a dithiol.'
change definition of GO:0000096 from 'The chemical reactions and pathways involving amino acids containing sulfur, comprising cysteine, homocysteine, methionine and selenocysteine.' to 'The chemical react

cmungall

cmungall

id,rdfs label,editor preferred term,has curation status,alternative term,definition,definition source,example of usage,term editor,editor note,curator note,ontology term requester,term tracker item,logical type,parent,output
ID,A rdfs:label,A editor preferred term,AI has curation status,A alternative term SPLIT=|,A definition SPLIT=|,A definition source SPLIT=|,A example of usage SPLIT=|,A term editor SPLIT=|,A editor note SPLIT=|,A curator note SPLIT=|,A ontology term requester SPLIT=|,A term tracker item SPLIT=|,CLASS_TYPE,C %,C has_specified_output some %
OBI:0003616,antibody purification of MHC class I protein complex,,,,"An antibody purification of MHC protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of MHC class I protein complex, while others contain impurities and are not of interest.",Randi Vita,,Randi Vita|Sebastian Duesing,,,,,equivalent,antibody purification of MHC protein complex,MHC class I protein complex
OBI:0003617

cmungall

ontology ID,label,editor preferred term,has curation status,alternative term,definition,definition source,example of usage,term editor,editor note,curator note,ontology term requester,term tracker item,logical type, specimen collection process,gross anatomical part,collection process input,URI
ID,A rdfs:label,A editor preferred term,AI has curation status,A alternative term,A definition,A definition source SPLIT=|,A example of usage SPLIT=|,A term editor SPLIT=|,A editor note SPLIT=|,A curator note SPLIT=|,A ontology term requester,A term tracker item,CLASS_TYPE,C specimen and (is_specified_output_of some %),C specimen and (is_specified_output_of some 'specimen collection process') and ('derives from' some %),C specimen and (is_specified_output_of some ('specimen collection process' and has_specified_input some %)),
OBI:0002500,amniotic fluid specimen,,ready for release,,A specimen that is derived from amniotic fluid.,"Chris Stoeckert, Penn Medicine Biobank",,Chris Stoeckert,,,,,equivalent,collecting specimen

cmungall

 uberon info .desc//p=i "anatomical structure" .not .desc//p=i,p [ "organism subdivision" "organ" ]
 
 http://purl.obolibrary.org/obo/UBERON_0003072 ! optic cup
http://purl.obolibrary.org/obo/UBERON_0008188 ! tendon of biceps brachii
http://purl.obolibrary.org/obo/UBERON_0005719 ! footplate apical ectodermal ridge
http://purl.obolibrary.org/obo/UBERON_0004468 ! set of muscles of vertebral column
http://purl.obolibrary.org/obo/UBERON_0009614 ! hindbrain neural plate
http://purl.obolibrary.org/obo/UBERON_0017615 ! vomerine dentition
http://purl.obolibrary.org/obo/UBERON_8480009 ! tendon of semitendinosus
http://purl.obolibrary.org/obo/UBERON_0005240 ! basal plate medulla oblongata

cmungall

http://purl.obolibrary.org/obo/UBERON_0003072 ! optic cup
http://purl.obolibrary.org/obo/UBERON_0008188 ! tendon of biceps brachii
http://purl.obolibrary.org/obo/UBERON_0005719 ! footplate apical ectodermal ridge
http://purl.obolibrary.org/obo/UBERON_0004468 ! set of muscles of vertebral column
http://purl.obolibrary.org/obo/UBERON_0009614 ! hindbrain neural plate
http://purl.obolibrary.org/obo/UBERON_0017615 ! vomerine dentition
http://purl.obolibrary.org/obo/UBERON_8480009 ! tendon of semitendinosus
http://purl.obolibrary.org/obo/UBERON_0005240 ! basal plate medulla oblongata
http://purl.obolibrary.org/obo/UBERON_0001999 ! iliopsoas
http://purl.obolibrary.org/obo/UBERON_0003854 ! spinal cord neural plate

cmungall

```sql
sqlite> attach 'db/orcid.db' as orcid_db;
sqlite> select * from contributor inner join orcid_db.orcid on (orcid.id=contributor.object) where orcid.label like 'Chris%';
obo:cl.owl|obo:cl.owl|dcterms:contributor|orcid:0000-0002-6601-2165||||orcid:0000-0002-6601-2165|Christopher J. Mungall
CL:0010001|CL:0010001|dcterms:contributor|orcid:0000-0002-6601-2165||||orcid:0000-0002-6601-2165|Christopher J. Mungall
CL:0010002|CL:0010002|dcterms:contributor|orcid:0000-0002-6601-2165||||orcid:0000-0002-6601-2165|Christopher J. Mungall
CL:0010003|CL:0010003|dcterms:contributor|orcid:0000-0002-6601-2165||||orcid:0000-0002-6601-2165|Christopher J. Mungall
CL:0010004|CL:0010004|dcterms:contributor|orcid:0000-0002-6601-2165||||orcid:0000-0002-6601-2165|Christopher J. Mungall
UBERON:0000093|UBERON:0000093|dcterms:contributor|orcid:0000-0002-6601-2165||||orcid:0000-0002-6601-2165|Christopher J. Mungall
UBERON:0000094|UBERON:0000094|dcterms:contributor|orcid:0000-0002-6601-2165||||orcid:0000-0002-6601-2165|Christopher J. M

cmungall

Using OAK to retrieve definitions

For more OAK examples, see

• https://incatools.github.io/ontology-access-kit/notebooks.html

Setup

$ pip install oaklib