cmungall

• [] ICD10CM:Q00-Q99 ! Congenital malformations, deformations and chromosomal abnormalities (Q00-Q99)
  • [i] ICD10CM:Q90-Q99 ! Chromosomal abnormalities, not elsewhere classified (Q90-Q99)
    • [i] ICD10CM:Q99 ! Other chromosome abnormalities, not elsewhere classified
      • [i] ICD10CM:Q99.9 ! Chromosomal abnormality, unspecified
      • [i] ICD10CM:Q99.8 ! Other specified chromosome abnormalities
      • [i] ICD10CM:Q99.2 ! Fragile X chromosome
      • [i] ICD10CM:Q99.1 ! 46, XX true hermaphrodite
      • [i] ICD10CM:Q99.0 ! Chimera 46, XX/46, XY
    • [i] ICD10CM:Q98 ! Other sex chromosome abnormalities, male phenotype, not elsewhere classified
• [i] ICD10CM:Q98.9 ! Sex chromosome abnormality, male phenotype, unspecified

cmungall

Normalizing YAML Formatting: yamlfix vs Prettier and the State of Standards

Executive summary

There is no broadly accepted, tool‑independent "canonical YAML formatting profile" comparable to Black for Python or gofmt for Go; each formatter defines its own style, and these styles are not standardized across tools. yamlfix and Prettier both provide opinionated YAML formatting, but they differ significantly in scope, defaults, configuration model, and how aggressively they normalize YAML constructs, meaning switching between them will generally cause large diffs rather than clean no‑ops. Some tools (e.g., Google’s yamlfmt and Carvel’s yamlfmt) describe their output as a "canonical form", but this is a per‑tool convention, not a YAML‑spec profile that other tools target. As a result, the practical way to avoid spurious diffs today is to pick a single formatter, standardize on its configuration across the repo, and wire it into pre‑commit/CI; changing formatter families later will almost certainly refor

cmungall

cmungall

/*

  Demonstration of a probabilistic ensemble scoring system,
  based on ontology FOL.

  This may be overkill for now, but it lends itself well to integrating
  more logical components, such as:

  - decomposing structures into has_part SMARTS structures
  - C3PO like mechanism that generates programs that derive more atomic predicates

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: dragon-ai@monarch-initiative.org
  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