Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / sorgerlab/indra issues and pull requests

#1461 - Add additional NCBITaxon-MeSH mappings

Pull Request - State: closed - Opened by bgyori 9 days ago

#1460 - Add SQLite-based ontology

Pull Request - State: open - Opened by bgyori about 2 months ago

#1459 - Correct the block in footer

Pull Request - State: closed - Opened by haohangyan about 2 months ago - 1 comment

#1458 - UI Fixes for db.indra.bio website

Pull Request - State: closed - Opened by haohangyan about 2 months ago - 1 comment

#1457 - Extend MeSH-PubMed and NCBI Taxonomy connection

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

#1456 - Update test for REST API

Pull Request - State: closed - Opened by kkaris 4 months ago

#1455 - Fix syntax warnings and styling

Pull Request - State: closed - Opened by bgyori 4 months ago

#1454 - Fixes to input processors due to changes in sources

Pull Request - State: closed - Opened by haohangyan 4 months ago

#1453 - Add fix for issue with latest SIGNOR release

Pull Request - State: closed - Opened by bgyori 4 months ago

#1452 - Update Flask, Flask Restx, unpin Gilda

Pull Request - State: closed - Opened by kkaris 5 months ago - 1 comment

#1451 - Documentation fixes

Pull Request - State: closed - Opened by bgyori 5 months ago

#1450 - Processor improvements

Pull Request - State: closed - Opened by bgyori 5 months ago

#1449 - Add client for RGD database

Pull Request - State: closed - Opened by bgyori 5 months ago

#1448 - Flask>=3 requires changes to flask-jwt-extended usage

Issue - State: closed - Opened by kkaris 5 months ago - 1 comment

#1447 - Networkx 3 compatibility

Pull Request - State: closed - Opened by kkaris 5 months ago

#1446 - Replace inspect.getargspec with inspect.getfullargspec

Pull Request - State: closed - Opened by kkaris 5 months ago - 2 comments

#1444 - Access Biopax

Issue - State: closed - Opened by Siliegia 6 months ago - 2 comments

#1443 - Extend to Python 3.12 compatibility

Pull Request - State: closed - Opened by bgyori 6 months ago

#1442 - Remove networkx<3 version constraint

Issue - State: closed - Opened by bgyori 6 months ago - 2 comments

#1441 - Remove pandas version restriction

Pull Request - State: closed - Opened by bgyori 6 months ago

#1440 - Move markupsafe version constraint

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

#1439 - Implement completing source counts in HTML assembler

Pull Request - State: closed - Opened by bgyori 8 months ago

#1438 - Having problem with Python 3.12 at macOS

Issue - State: closed - Opened by muhammadshoaib 9 months ago - 4 comments

#1437 - Remove lib2to3 logging patch

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

#1436 - Update resource files

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

#1435 - Reimplement cBioPortal client for new API

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

#1434 - cBioPortal legacy API is shut down

Issue - State: closed - Opened by kkaris 10 months ago - 2 comments

#1433 - Remove mesh cycle from bio-ontology

Pull Request - State: closed - Opened by kkaris 10 months ago - 1 comment

#1432 - Add version to file docstring and log message in bio ontology CLI

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

#1431 - Update MeSH to 2024

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

#1430 - Improve PubMed metadata extraction handling

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

#1429 - Add Ensembl info for MGI genes

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

#1428 - Pubmed retractions

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

#1426 - Add more robust retry to the pubmed client's send_request

Pull Request - State: closed - Opened by kkaris 12 months ago - 2 comments

#1425 - Use RTD config for docs build

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

#1424 - Implement retrieving more than 10k PMIDs and all metadata

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

#1423 - Db sources updates

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

#1422 - RLIMS-P invalid statement error

Issue - State: closed - Opened by kkaris about 1 year ago - 2 comments

#1421 - HPRD is now behind login, server responds with 500

Issue - State: closed - Opened by kkaris about 1 year ago - 1 comment

#1420 - CausalBioNet processing - KeyError while processing jgif file

Issue - State: closed - Opened by kkaris about 1 year ago - 3 comments

#1419 - Signor processor error

Issue - State: closed - Opened by kkaris about 1 year ago - 2 comments

#1418 - Ubibrowser KeyError

Issue - State: closed - Opened by kkaris about 1 year ago - 3 comments

#1417 - Update dependencies

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

#1416 - Journal info

Pull Request - State: closed - Opened by kkaris over 1 year ago - 4 comments

#1415 - Update HGNC resource

Pull Request - State: closed - Opened by bgyori over 1 year ago

#1414 - Handle underscores in agent IDs for DB query

Pull Request - State: closed - Opened by bgyori over 1 year ago

#1413 - PubMed XML save option

Pull Request - State: closed - Opened by bgyori over 1 year ago

#1412 - Add coordinate info to Agent extraction endpoints from readers

Pull Request - State: closed - Opened by bgyori over 1 year ago

#1411 - Standardize MeSH 2022

Pull Request - State: closed - Opened by cthoyt over 1 year ago

#1410 - Add Python 3.10 testing

Pull Request - State: closed - Opened by bgyori over 1 year ago

#1409 - Update SIGNOR processor and FamPlex

Pull Request - State: closed - Opened by bgyori over 1 year ago

#1408 - Update documentation

Pull Request - State: closed - Opened by cthoyt over 1 year ago

#1407 - Get article references, either just PMIDs or details

Pull Request - State: closed - Opened by pagreene over 1 year ago

#1406 - Allow enhanced author parsing

Pull Request - State: closed - Opened by pagreene over 1 year ago

#1405 - Migrate testing from nosetests to pytest

Pull Request - State: closed - Opened by bgyori over 1 year ago

#1404 - Python and pandas compatibility adjustments

Pull Request - State: closed - Opened by bgyori over 1 year ago

#1403 - indra literature id_lookup bug

Issue - State: closed - Opened by Crispae over 1 year ago - 4 comments

#1402 - Various fixes and improvements

Pull Request - State: closed - Opened by bgyori over 1 year ago

#1401 - using a identifiers.org namespace that is not embedded in INDRA

Issue - State: closed - Opened by guerrerosimonl almost 2 years ago - 2 comments

#1400 - Allow extracting all Agents from Reach entities

Pull Request - State: closed - Opened by bgyori almost 2 years ago

#1399 - Propagate section information from new Reach implementation

Pull Request - State: closed - Opened by bgyori almost 2 years ago

#1398 - Extend INDRA for cellular communication

Issue - State: open - Opened by Siliegia about 2 years ago - 2 comments

#1397 - Single quotes don't work for Windows

Pull Request - State: closed - Opened by kwalcock about 2 years ago - 1 comment

#1396 - Add optional residue/position feature to CountScorer

Pull Request - State: closed - Opened by johnbachman about 2 years ago

#1395 - Update MeSH resources and ontology

Pull Request - State: closed - Opened by bgyori about 2 years ago

#1394 - Representing fusion proteins

Issue - State: open - Opened by cthoyt about 2 years ago

#1393 - Implement input API and processor for EVEX database

Pull Request - State: open - Opened by bgyori about 2 years ago

#1392 - Improve BioPAX conversion processing and extend API

Pull Request - State: closed - Opened by bgyori about 2 years ago

#1391 - Implement client for MGI resources

Pull Request - State: closed - Opened by bgyori about 2 years ago

#1390 - Handle more UP/HGNC corner cases in BioPAX

Pull Request - State: closed - Opened by bgyori about 2 years ago

#1389 - Problem with get_biopax_stmts() with neighborhood option

Issue - State: closed - Opened by devonjkohler about 2 years ago - 2 comments

#1388 - Question about section type in REACH processor

Issue - State: closed - Opened by sanyabt over 2 years ago - 9 comments

#1387 - Patch BioGRID processsor to work with old tab2 data.

Pull Request - State: closed - Opened by johnbachman over 2 years ago

#1386 - Eliminate isa/partof ontology cycles

Pull Request - State: closed - Opened by bgyori over 2 years ago - 1 comment

#1385 - FamPlex resource update

Pull Request - State: closed - Opened by bgyori over 2 years ago

#1384 - Improvements in source processing

Pull Request - State: closed - Opened by bgyori over 2 years ago

#1383 - Generalize prefix separator handling in Bioregistry

Pull Request - State: closed - Opened by bgyori over 2 years ago

#1382 - Add module for interfacing with Bioregistry

Pull Request - State: closed - Opened by bgyori over 2 years ago

#1381 - Update SIGNOR processor

Pull Request - State: closed - Opened by bgyori over 2 years ago

#1380 - Add SemRep API and processor

Pull Request - State: closed - Opened by bgyori over 2 years ago

#1379 - Add xrefs endpoint using IndraOntology.get_mappings()

Pull Request - State: closed - Opened by kkaris over 2 years ago

#1378 - Fix handling of xrefs from OBO

Pull Request - State: open - Opened by bgyori over 2 years ago - 2 comments

#1377 - Update Biomappings

Pull Request - State: closed - Opened by bgyori over 2 years ago

#1376 - Integrate mappings provided by MeSH to CAS

Pull Request - State: closed - Opened by bgyori over 2 years ago

#1375 - Expose refinement finding and deserialization functions

Pull Request - State: closed - Opened by bgyori over 2 years ago

#1374 - Add option for local text content DB for grounding mapping

Pull Request - State: closed - Opened by bgyori over 2 years ago

#1373 - Add EC client

Pull Request - State: closed - Opened by cthoyt over 2 years ago

#1372 - Add base assembler class

Pull Request - State: closed - Opened by cthoyt over 2 years ago - 2 comments

#1371 - [WIP] add FMA ontology

Pull Request - State: open - Opened by bgyori over 2 years ago

#1370 - Pick up quantifier arguments from Eidos

Pull Request - State: closed - Opened by bgyori over 2 years ago

#1369 - Pip backtracking during install

Issue - State: closed - Opened by bgyori almost 3 years ago - 3 comments

#1368 - Extend ontology with replacement relations

Pull Request - State: closed - Opened by bgyori almost 3 years ago

#1367 - Add enzyme code queries to HGNC client

Pull Request - State: closed - Opened by cthoyt almost 3 years ago - 1 comment

#1366 - Adding new source Atlas of cancer signaling network (ACSN) DB

Pull Request - State: closed - Opened by samuelbunga almost 3 years ago

#1365 - Modify filter by curation

Pull Request - State: closed - Opened by dianakolusheva almost 3 years ago

#1364 - Update path to Eidos JSON-LD exporter

Pull Request - State: closed - Opened by bgyori almost 3 years ago

#1363 - Add source module for UbiBrowser

Pull Request - State: closed - Opened by bgyori almost 3 years ago

#1362 - Add ECOTOX Knowledgebase

Issue - State: open - Opened by cthoyt almost 3 years ago
Labels: source