biolink/ontobio issues and pull requests

#696 - update relation map in relations.py to match expectations

Pull Request - State: open - Opened by sierra-moxon 27 days ago - 1 comment

#695 - rewrite gpi path to use provide GPI if provided, and create if needed

Pull Request - State: closed - Opened by sierra-moxon about 2 months ago

#694 - add last debugging output via click instead of logger

Pull Request - State: closed - Opened by sierra-moxon about 2 months ago

#693 - Debugging missing gpi

Pull Request - State: closed - Opened by sierra-moxon about 2 months ago

#692 - For #2360 - Updated to handle DBs without id syntax pattern

Pull Request - State: closed - Opened by mugitty about 2 months ago - 2 comments

#691 - Replace hegroup sparql endpoint URL with rdf.geneontology.org/sparql

Pull Request - State: closed - Opened by sierra-moxon about 2 months ago

#690 - Bump cryptography from 43.0.0 to 43.0.1

Pull Request - State: closed - Opened by dependabot[bot] 2 months ago
Labels: dependencies

#689 - Current version of ontobio, in some cases, has trouble parsing GAF(?)

Issue - State: open - Opened by kltm 3 months ago - 1 comment
Labels: bug

#688 - ontobio is not HTTPS-safe

Issue - State: open - Opened by kltm 3 months ago - 1 comment
Labels: bug

#687 - revert autoversion, set up setup.py for a manual push to pypi

Pull Request - State: closed - Opened by sierra-moxon 3 months ago

#686 - Pypi publish

Pull Request - State: closed - Opened by sierra-moxon 3 months ago - 1 comment

#685 - add an optional test to make sure full validate produce is run when l…

Pull Request - State: closed - Opened by sierra-moxon 3 months ago - 3 comments

#684 - fixes pipeline issue 383 - gpad 1.2 should have `!gpa-version` in the header, not `!gpad-version` in the header

Pull Request - State: closed - Opened by sierra-moxon 3 months ago

#683 - force GAF 2.2 output, instead of taking version from input GAFs - fixing the chickens

Pull Request - State: closed - Opened by sierra-moxon 3 months ago

#682 - fixes pipeline issue 380 by editing the header, taxon, type of the GP…

Pull Request - State: closed - Opened by sierra-moxon 3 months ago

#681 - swaps subject with gene when subject is PR isoform

Pull Request - State: closed - Opened by sierra-moxon 3 months ago

#680 - add groups to gitignore, parse and refactor isoforms in gaf files, ad…

Pull Request - State: closed - Opened by sierra-moxon 4 months ago

#679 - For #2210

Pull Request - State: closed - Opened by mugitty 4 months ago - 2 comments

#678 - For #2210

Pull Request - State: closed - Opened by mugitty 4 months ago - 1 comment

#677 - Go site 2210 gorule 0000027 must check dbs are in the db xref file

Pull Request - State: closed - Opened by mugitty 4 months ago - 7 comments

#676 - Go site 2246 gorule 0000001 rnac rna types are getting mangled

Pull Request - State: closed - Opened by mugitty 5 months ago - 7 comments

#675 - Minimal changes for gpad gpi 2 0

Pull Request - State: closed - Opened by sierra-moxon 6 months ago

#674 - Go site 676 gorule 0000022 check for retracted publications

Pull Request - State: closed - Opened by mugitty 6 months ago - 4 comments

#673 - For #2273 Fix path

Pull Request - State: closed - Opened by mugitty 7 months ago - 3 comments

#672 - For #2273

Pull Request - State: closed - Opened by mugitty 7 months ago

#671 - ontobio pull request failing workflow actions due to Monarch

Issue - State: open - Opened by mugitty 7 months ago - 1 comment

#670 - For #2108

Pull Request - State: closed - Opened by mugitty 7 months ago - 1 comment

#669 - For #887

Pull Request - State: closed - Opened by mugitty 8 months ago - 1 comment

#668 - For #2108

Pull Request - State: closed - Opened by mugitty 9 months ago

#667 - For #1553

Pull Request - State: closed - Opened by mugitty 9 months ago - 2 comments

#666 - For #2064 - Added check for pipe in gene symbol

Pull Request - State: closed - Opened by mugitty 9 months ago - 3 comments

#665 - Add underscore to GO_REF:0000033

Pull Request - State: closed - Opened by dustine32 10 months ago

#664 - remove -aux from golr url

Pull Request - State: closed - Opened by sierra-moxon 10 months ago

#663 - fix header emitted from gpad writer to match 2.0 specifications

Pull Request - State: closed - Opened by sierra-moxon 11 months ago - 3 comments

#662 - For #346

Pull Request - State: closed - Opened by mugitty 11 months ago

#661 - For #1658

Pull Request - State: closed - Opened by mugitty 11 months ago

#660 - null check with_from items

Pull Request - State: closed - Opened by sierra-moxon 12 months ago - 3 comments

#659 - For #2131

Pull Request - State: closed - Opened by mugitty 12 months ago

#658 - For #2124 Disable Gorule51

Pull Request - State: closed - Opened by mugitty 12 months ago - 1 comment

#657 - For #2175 validate go id

Pull Request - State: closed - Opened by mugitty 12 months ago - 1 comment

#656 - For #1523 check for unique GO ID

Pull Request - State: closed - Opened by mugitty 12 months ago - 1 comment

#655 - For #2072

Pull Request - State: closed - Opened by mugitty 12 months ago

#654 - For #2081 repair goid, with/from and extension before running gorule …

Pull Request - State: closed - Opened by mugitty about 1 year ago - 4 comments

#653 - For #2093

Pull Request - State: closed - Opened by mugitty about 1 year ago - 8 comments

#652 - sqlite3.DatabaseError: file is not a database

Issue - State: open - Opened by AITCM about 1 year ago

#651 - For #2079 added check for binding

Pull Request - State: closed - Opened by mugitty about 1 year ago - 1 comment

#650 - For #1658

Pull Request - State: closed - Opened by mugitty about 1 year ago - 8 comments

#649 - Reverting FAIL to OKAY since obsolete terms have no namespace

Pull Request - State: closed - Opened by dustine32 about 1 year ago

#648 - Handle GPI label merge for geneontology/go-releases#50

Pull Request - State: closed - Opened by dustine32 about 1 year ago - 3 comments

#647 - For #2070 check for numeric taxon

Pull Request - State: closed - Opened by mugitty about 1 year ago - 1 comment

#646 - For #2002 updated due to change in requirements

Pull Request - State: closed - Opened by mugitty about 1 year ago - 1 comment

#645 - Go site 2066 gorule 0000001 invalid taxon id 0

Pull Request - State: closed - Opened by mugitty about 1 year ago

#644 - For #2058 gorule-0000051 first implementation

Pull Request - State: closed - Opened by mugitty about 1 year ago

#643 - For #2049 Added check for DB object symbol

Pull Request - State: closed - Opened by mugitty about 1 year ago

#642 - For #2038 Changed to error from warning

Pull Request - State: closed - Opened by mugitty about 1 year ago

#641 - Update pypi release instructions

Pull Request - State: closed - Opened by sierra-moxon about 1 year ago - 1 comment

#640 - For #844

Pull Request - State: closed - Opened by mugitty about 1 year ago