geneontology/gocamgen issues and pull requests

#94 - Processing annotation contributors for multiple GPAD lines with single annotation id

Issue - State: open - Opened by vanaukenk over 3 years ago - 5 comments
Labels: Annotation Properties

#93 - Set import model states to production so annotations are in GPAD outputs from dev

Issue - State: closed - Opened by ukemi over 3 years ago - 5 comments
Labels: GPAD output

#92 - Comment missing some text from the GPAD

Issue - State: open - Opened by ukemi over 3 years ago - 1 comment

#91 - Param to set modelstate

Issue - State: closed - Opened by dustine32 over 3 years ago - 1 comment

#90 - Add gene symbol to model title

Issue - State: closed - Opened by dustine32 over 3 years ago - 14 comments

#89 - Add providedBy to all individuals

Issue - State: closed - Opened by dustine32 over 3 years ago - 2 comments

#88 - Collapse comma-delimited objects of chain relations

Issue - State: open - Opened by ukemi over 3 years ago

#87 - Emit comment in annotation properties

Issue - State: closed - Opened by dustine32 over 3 years ago - 1 comment

#86 - Add date and contributor to ALL annotation individuals? Not just evidence and Axiom?

Issue - State: closed - Opened by dustine32 over 3 years ago - 4 comments

#85 - Handling interacting taxon data

Issue - State: open - Opened by dustine32 almost 4 years ago

#84 - Handle pipe-separation in translation of with/from field

Issue - State: open - Opened by dustine32 over 4 years ago - 1 comment

#83 - Proteoforms shouldn't be split into separate models

Issue - State: closed - Opened by ukemi over 4 years ago - 14 comments

#82 - Write translated models out in N-Quads format

Issue - State: closed - Opened by dustine32 over 4 years ago - 1 comment

#81 - Create test files for WB import

Issue - State: open - Opened by vanaukenk over 4 years ago - 12 comments

#80 - add taxon metadata for each model

Issue - State: closed - Opened by goodb over 4 years ago - 5 comments

#79 - Resolve Shex failures in MGI annotations due to invalid identifiers for binding input

Issue - State: open - Opened by ukemi over 4 years ago - 38 comments

#78 - No extension is an island

Issue - State: open - Opened by ukemi over 4 years ago - 4 comments

#77 - Create test files for additional annotation metadata

Issue - State: open - Opened by ukemi over 4 years ago - 31 comments

#76 - Update formatted_ext_patterns.tsv

Pull Request - State: closed - Opened by dustine32 almost 5 years ago

#75 - Update extension validation rules for acts_o_population_of

Issue - State: open - Opened by dustine32 almost 5 years ago - 3 comments
Labels: annotation extensions

#74 - Update formatted_ext_patterns.tsv

Pull Request - State: closed - Opened by dustine32 almost 5 years ago

#73 - Update extension validation rules TSV

Issue - State: closed - Opened by dustine32 almost 5 years ago
Labels: annotation extensions

#72 - Update formatted_ext_patterns.tsv

Pull Request - State: closed - Opened by vanaukenk almost 5 years ago - 2 comments

#71 - Update formatted_ext_patterns.tsv

Pull Request - State: closed - Opened by vanaukenk almost 5 years ago

#70 - Refactor gocamgen to make it usable in GO pipeline (ontobio)

Issue - State: open - Opened by dustine32 almost 5 years ago

#69 - Update formatted_ext_patterns.tsv

Pull Request - State: closed - Opened by dustine32 almost 5 years ago - 5 comments

#68 - Update rules spreadsheet

Issue - State: open - Opened by dustine32 almost 5 years ago - 21 comments
Labels: annotation extensions

#67 - Removed ISO from unwanted_evidence_codes in mgi.yaml for issue #37

Pull Request - State: open - Opened by dustine32 almost 5 years ago

#66 - Issue 63 valid exts

Pull Request - State: closed - Opened by dustine32 almost 5 years ago - 2 comments

#65 - Issue 25 occurs in

Pull Request - State: closed - Opened by dustine32 almost 5 years ago

#64 - Translate has_regulation_target to has_input for regulation of gene expression annotations

Issue - State: open - Opened by dustine32 almost 5 years ago - 4 comments

#63 - Regularly generate "bad extensions" reports of MGI GPAD

Issue - State: open - Opened by dustine32 almost 5 years ago - 27 comments

#62 - 'results in' extensions that would need new ontology terms

Issue - State: open - Opened by vanaukenk almost 5 years ago - 4 comments
Labels: annotation extensions, ShEx

#61 - Ontology currently causes MGI:MGI:1336882 model to fail ShEx

Issue - State: open - Opened by dustine32 almost 5 years ago
Labels: ShEx

#60 - Modeling 'regulates o occurs in' annotation extensions

Issue - State: open - Opened by vanaukenk about 5 years ago - 6 comments

#59 - Update formatted_ext_patterns.tsv for issue #58

Pull Request - State: closed - Opened by dustine32 about 5 years ago - 5 comments

#58 - Update rules in formatted_ext_patterns.tsv

Issue - State: closed - Opened by dustine32 about 5 years ago - 1 comment
Labels: annotation extensions

#57 - Map ro ext relations

Pull Request - State: closed - Opened by dustine32 about 5 years ago

#56 - Update formatted_ext_patterns.tsv

Pull Request - State: closed - Opened by vanaukenk about 5 years ago - 2 comments

#55 - Update formatted_ext_patterns.tsv

Pull Request - State: closed - Opened by vanaukenk about 5 years ago

#54 - Update formatted_ext_patterns.tsv

Pull Request - State: closed - Opened by vanaukenk about 5 years ago

#53 - Validate models against GO-CAM spec in ShEx

Issue - State: open - Opened by dustine32 about 5 years ago
Labels: ShEx

#52 - Refactor code to use a reusable gocam data model

Issue - State: open - Opened by lpalbou about 5 years ago

#51 - Simple mapping of extension relations to ontologies (RO/BFO)

Issue - State: open - Opened by dustine32 over 5 years ago - 10 comments
Labels: annotation extensions

#50 - Generalize the 'has input' conversion for 'binding' and all children

Issue - State: open - Opened by vanaukenk over 5 years ago - 8 comments
Labels: ready to test on noctua-dev, ready to test on USC server

#49 - change has_direct_input to has_input for imported BP and MF annotations

Issue - State: closed - Opened by vanaukenk over 5 years ago - 3 comments
Labels: ready to test on noctua-dev, ready to test on USC server, annotation extensions

#48 - 'With' field info missing from IMP annotation

Issue - State: closed - Opened by ukemi over 5 years ago - 13 comments
Labels: ready to test on USC server, With/From

#47 - Merge imports with existing gene-centric models

Issue - State: open - Opened by vanaukenk over 5 years ago - 8 comments
Labels: question

#46 - Issue 44 and some other things

Pull Request - State: closed - Opened by dustine32 over 5 years ago

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

Issue - State: open - Opened by dustine32 over 5 years ago - 19 comments
Labels: ready to test on noctua-dev, ready to test on USC server

#44 - Translate has_regulation_target extensions

Issue - State: open - Opened by dustine32 over 5 years ago - 18 comments
Labels: ready to test on noctua-dev, ready to test on USC server, annotation extensions

#43 - Use gene identifier as Noctua model ID

Issue - State: open - Opened by dustine32 over 5 years ago

#42 - Extensions spreadsheet generation and model import should use same filtering logic

Issue - State: closed - Opened by dustine32 over 5 years ago - 2 comments

#41 - WB:WBGene00006498 model is missing all BP annotations from WB

Issue - State: closed - Opened by vanaukenk over 5 years ago - 4 comments
Labels: ready to test on noctua-dev

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

Issue - State: open - Opened by vanaukenk over 5 years ago - 11 comments
Labels: ready to test on noctua-dev, ready to test on USC server, annotation extensions