geneontology/gocamgen

Issues

• Filtering MGI: Allow ISO if Assigned_by=MGI

  #37 opened 3 months ago by dustine32
  38

• Processing annotation contributors for multiple GPAD lines with single annotation id

  #94 opened 3 years ago by vanaukenk
  5

• Merge imports with existing gene-centric models

  #47 opened 5 years ago by vanaukenk
  8

• Create test files for WB import

  #81 opened 4 years ago by vanaukenk
  12

• Param to set modelstate

  #91 opened 3 years ago by dustine32
  1

• Set import model states to production so annotations are in GPAD outputs from dev

  #93 opened 3 years ago by ukemi
  5

• Add gene symbol to model title

  #90 opened 3 years ago by dustine32
  14

• Paper value import when pipe-separated entry in GPAD

  #31 opened 6 years ago by vanaukenk
  9

• Comment missing some text from the GPAD

  #92 opened 3 years ago by ukemi
  1

• add taxon metadata for each model

  #80 opened 3 years ago by goodb
  5

• Proteoforms shouldn't be split into separate models

  #83 opened 3 years ago by ukemi
  14

• Add date and contributor to ALL annotation individuals? Not just evidence and Axiom?

  #86 opened 3 years ago by dustine32
  4

• Add providedBy to all individuals

  #89 opened 3 years ago by dustine32
  2

• Collapse comma-delimited objects of chain relations

  #88 opened 3 years ago by ukemi
  0

• Emit comment in annotation properties

  #87 opened 4 years ago by dustine32
  1

• Create test files for additional annotation metadata

  #77 opened 5 years ago by ukemi
  31

• Resolve Shex failures in MGI annotations due to invalid identifiers for binding input

  #79 opened 5 years ago by ukemi
  38

• Handling interacting taxon data

  #85 opened 4 years ago by dustine32
  0

• Modeling 'regulates o occurs in' annotation extensions

  #60 opened 5 years ago by vanaukenk
  6

• Write translated models out in N-Quads format

  #82 opened 4 years ago by dustine32
  1

• Handle pipe-separation in translation of with/from field

  #84 opened 4 years ago by dustine32
  1

• Translate has_regulation_target to has_input for regulation of gene expression annotations

  #64 opened 5 years ago by dustine32
  4

• Translate has_regulation_target extensions

  #44 opened 5 years ago by dustine32
  18

• No extension is an island

  #78 opened 5 years ago by ukemi
  4

• Regularly generate "bad extensions" reports of MGI GPAD

  #63 opened 5 years ago by dustine32
  27

• Update extension validation rules for acts_o_population_of

  #75 opened 5 years ago by dustine32
  3

• Update extension validation rules TSV

  #73 opened 5 years ago by dustine32
  0

• Update rules spreadsheet

  #68 opened 5 years ago by dustine32
  21

• Refactor gocamgen to make it usable in GO pipeline (ontobio)

  #70 opened 5 years ago by dustine32
  0

• Generalize the 'has input' conversion for 'binding' and all children

  #50 opened 5 years ago by vanaukenk
  8

• Update rules in formatted_ext_patterns.tsv

  #58 opened 5 years ago by dustine32
  1

• 'results in' extensions that would need new ontology terms

  #62 opened 5 years ago by vanaukenk
  4

• Create progress reports that include GPAD lines for annotations that don't get converted

  #36 opened 6 years ago by vanaukenk
  1

• Validate models against GO-CAM spec in ShEx

  #53 opened 5 years ago by dustine32
  0

• Ontology currently causes MGI:MGI:1336882 model to fail ShEx

  #61 opened 5 years ago by dustine32
  0

• Pipe-separated annotation extensions should result in separate GO-CAM annotations

  #40 opened 6 years ago by vanaukenk
  11

• GP acts_upstream_of_or_within BP -> root MF enabled by GP causally_upstream_of_or_within BP

  #38 opened 5 years ago by vanaukenk
  6

• change has_direct_input to has_input for imported BP and MF annotations

  #49 opened 5 years ago by vanaukenk
  3

• 'With' field info missing from IMP annotation

  #48 opened 5 years ago by ukemi
  13

• Refactor code to use a reusable gocam data model

  #52 opened 5 years ago by lpalbou
  0

• Simple mapping of extension relations to ontologies (RO/BFO)

  #51 opened 5 years ago by dustine32
  10

• Define what qualifies a GPAD line as a distinct assertion individual in GO-CAM

  #45 opened 5 years ago by dustine32
  19

• Extensions spreadsheet generation and model import should use same filtering logic

  #42 opened 5 years ago by dustine32
  2

• WB:WBGene00006498 model is missing all BP annotations from WB

  #41 opened 5 years ago by vanaukenk
  4

• Inputs with a contributes_to MF need to be associated with the MF, not the GP

  #39 opened 5 years ago by vanaukenk
  9

• Use gene identifier as Noctua model ID

  #43 opened 5 years ago by dustine32
  0

• Genes with all root node annotations should all be in one individual

  #32 opened 6 years ago by vanaukenk
  0

• Merged triples creating "orphaned" axioms/evidence

  #34 opened 6 years ago by dustine32
  6

• Use inter-ontology relations to link manual annotations

  #33 opened 6 years ago by vanaukenk
  1

• Include annotations using high throughput (HTP) manual assertion evidence codes in import

  #35 opened 6 years ago by vanaukenk
  2