Ecosyste.ms: Issues

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

GitHub / gyorilab/gilda issues and pull requests

#152 - Consider raw words for stoplist

Pull Request - State: open - Opened by tomo-oga 3 months ago

#151 - Update tests.yml to use new punkt file from NLTK

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

#150 - Word process and result table generation

Pull Request - State: open - Opened by haohangyan 5 months ago

#149 - Add functions to generate NER output result table

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

#148 - NER Benchmark Script

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

#147 - Use coordinates in custom sentence split function

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

#146 - Improve NER with word tokenization

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

#145 - Web and REST service expansion

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

#144 - Add an extra word to README

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

#142 - Annotate should return a list of ScoredMatches with each entry

Issue - State: closed - Opened by bgyori 7 months ago - 1 comment

#141 - Implement context text for annotation and fix capitalization

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

#140 - Improve MeSH mappings

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

#139 - Upgrade for Python 3.12 compatibility

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

#138 - Allow for 'classic' gunicorn running

Pull Request - State: closed - Opened by kkaris 9 months ago - 1 comment

#137 - indra/gilda incompatible dependencies

Issue - State: closed - Opened by jim-sheldon 10 months ago - 2 comments
Labels: bug

#135 - Add default grounding resources to README

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

#134 - Update readme with entities groundable

Issue - State: closed - Opened by YojanaGadiya 11 months ago

#133 - Add more careful norm_text check

Pull Request - State: open - Opened by cthoyt 12 months ago - 5 comments

#132 - Loading remote indexes

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

#131 - Update footer text

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

#130 - Make instantiation of Grounder more flexible

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

#129 - Add convenience function `Grounder.ground_best`

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

#128 - Update terms with latest resources

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

#127 - Improve safety of NER build

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

#126 - Expose `dump_terms` from top level

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

#125 - Update flask and flask-restx dependencies

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

#124 - Update docs

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

#123 - Listing the common biological entites, which glida fails to normalize

Issue - State: open - Opened by Crispae about 1 year ago - 3 comments

#122 - Strip certain special characters

Issue - State: open - Opened by kkaris over 1 year ago

#121 - Include Python 3.11 in testing

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

#120 - Enable returning all NER results

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

#119 - Make web UI dependencies optional

Pull Request - State: closed - Opened by cthoyt over 1 year ago - 5 comments

#118 - Add NER tutorial and update documentation configuration

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

#117 - Move dump_terms()

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

#116 - Make term prefix prioritization configurable

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

#115 - Add NER

Pull Request - State: closed - Opened by cthoyt over 1 year ago - 3 comments

#114 - Update signature of annotate()

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

#113 - Return ScoredMatch objects in annotate()

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

#112 - Improve filtering of duplicates

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

#111 - Fix invalid Adeft IDs

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

#110 - Make requirement `obonet` optional

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

#109 - Enable passing custom terms to web application

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

#108 - Add function to yield Terms from file

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

#107 - Add pandas DataFrame utilities

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

#106 - Strip whitespaces for input

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

#105 - Improve depluralization

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

#104 - Fix double whitespace and typo in docstring

Pull Request - State: closed - Opened by EFord36 about 2 years ago - 4 comments

#103 - Move `filter_out_duplicates` function

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

#102 - Update resources

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

#101 - Test branch

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

#100 - Add batched grounding endpoint to web service

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

#99 - Use legacy UniProt service to generate terms

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

#98 - Term `jq1` missing `entry_name`?

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

#97 - Implement optional SQLite back-end

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

#96 - Lazy loading for disambiguation models

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

#95 - High memory footprint

Issue - State: closed - Opened by ravwojdyla over 2 years ago - 33 comments

#94 - Generalizations to benchmarks

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

#93 - Split disambiguation evaluation

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

#92 - Update Gilda documentation and add custom grounder demo notebook

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

#91 - Extend grounder API

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

#90 - Add form to matches page

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

#89 - Expose all groundings and namespaces, and allow filtering

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

#88 - Update BioID evaluation and add diff tool

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

#87 - Add synonyms from Entrez for human genes

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

#86 - Further artifacts for Google add-on

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

#85 - Add HGNC alias names as synonyms

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

#84 - Add Google Docs add-on

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

#83 - Optimizations

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

#82 - Add model training notebook

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

#81 - Add more information to web UI via modals

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

#80 - Improve traceability of matches

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

#79 - Enable date context to improve lookup accuracy

Issue - State: open - Opened by dhimmel almost 3 years ago - 1 comment

#78 - HGNC gene name alias "FP prostanoid receptor" is not matched

Issue - State: closed - Opened by dhimmel about 3 years ago - 5 comments

#77 - Some challenging gene/protein names

Issue - State: open - Opened by dhimmel about 3 years ago - 1 comment

#76 - Implement normalization for unicode characters

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

#75 - Exclude entity synonyms for activity processes

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

#74 - Handle another corner case in UP synonym processing

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

#73 - Improve synonym extraction from UniProt

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

#72 - Rename assertion to curated and previous to former_name

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

#71 - Investigate additional benchmarks

Issue - State: open - Opened by cthoyt about 3 years ago

#70 - Add MONDO terms

Pull Request - State: open - Opened by cthoyt over 3 years ago - 1 comment

#69 - Resource update with improved term processing

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

#68 - Add testing on py310

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

#67 - Enable specifying query in path

Pull Request - State: closed - Opened by cthoyt over 3 years ago

#66 - Add unit tests for the Gilda web app

Pull Request - State: closed - Opened by cthoyt over 3 years ago

#65 - Handle roman vs arabic numerals

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

#64 - Handle roman numerals

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

#63 - How to subset matches to specific entity types?

Issue - State: closed - Opened by dhimmel over 3 years ago - 6 comments

#62 - Handle accented characters

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

#61 - Compress and add header to grounding terms file

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

#60 - How to access column names for `grounding_terms.tsv`?

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

#59 - Compress gilda.resources data files (gilda_models.pkl and grounding_terms.tsv)

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

#58 - API docs improvements

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

#57 - Accept query string as URL

Issue - State: closed - Opened by cthoyt over 3 years ago

#56 - Keep track of source versions

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

#55 - Generate Swagger UI with `flask_restx`

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

#54 - Add swagger/openapi spec

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

#53 - Add Dockerfile

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