Ecosyste.ms: Issues

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GitHub / renaud/neuroNER issues and pull requests

#64 - SEVERE: Can't find bluima/neuroner

Issue - State: open - Opened by sepehrgolriz over 4 years ago

#63 - Add cells from regenbase ontology

Issue - State: open - Opened by stripathy over 8 years ago

#62 - Plan for ontologizing neuroNER

Issue - State: open - Opened by dosumis over 8 years ago - 10 comments

#61 - Pypi updates

Pull Request - State: open - Opened by stripathy over 8 years ago

#60 - get DB crossrefs for UBERON term

Issue - State: closed - Opened by stripathy over 8 years ago - 2 comments

#59 - export uberon structure name as exact synonym .obo file

Issue - State: closed - Opened by stripathy over 8 years ago - 4 comments

#58 - updates to obo resource files breaks sherlok parsing

Issue - State: open - Opened by stripathy over 8 years ago - 2 comments

#57 - variants of allen brain regions

Issue - State: open - Opened by tgbugs over 8 years ago - 14 comments

#56 - switch ontology resource backend to .ttl from .obo

Issue - State: open - Opened by stripathy almost 9 years ago - 1 comment

#55 - lower number of UNKN brain regions

Issue - State: open - Opened by renaud almost 9 years ago

#54 - migrate to UBERON for brain regions and synonyms

Issue - State: open - Opened by stripathy almost 9 years ago - 16 comments

#53 - create an alpha release of neuroNER and put on pip

Issue - State: open - Opened by stripathy almost 9 years ago - 5 comments

#52 - consider using neuroelectro to show neuroNER queries

Issue - State: open - Opened by stripathy almost 9 years ago - 2 comments

#51 - benchmark neuroNER coverage against existing ontologies

Issue - State: open - Opened by stripathy almost 9 years ago - 2 comments

#50 - improve synonyms for brain regions

Issue - State: open - Opened by stripathy almost 9 years ago

#49 - cleanup of obo files

Pull Request - State: closed - Opened by tgbugs almost 9 years ago - 1 comment

#48 - Leverage the work done in OBO community to build interoperable ontologies

Issue - State: open - Opened by cmungall almost 9 years ago - 12 comments

#47 - NBC wrongly recognized as protein

Issue - State: closed - Opened by renaud almost 9 years ago

#44 - only keep a single ontology term corresponding to the same span of text

Issue - State: closed - Opened by stripathy almost 9 years ago - 1 comment
Labels: normalization

#43 - consider giving short names to ontology terms, then cause use normalization for term shortening

Issue - State: closed - Opened by stripathy almost 9 years ago
Labels: normalization

#42 - traverse layer ontology and return major parts along with subparts

Issue - State: closed - Opened by stripathy almost 9 years ago
Labels: normalization

#41 - return ABA major brain region along with found sub regions

Issue - State: closed - Opened by stripathy almost 9 years ago
Labels: normalization

#40 - Adding regions_lfrench.mappings.csv

Pull Request - State: open - Opened by leonfrench about 9 years ago

#39 - why is layer not being found here?

Issue - State: closed - Opened by stripathy about 9 years ago - 1 comment

#38 - Encode the various ways of encoding a hyphen sign

Issue - State: open - Opened by stripathy about 9 years ago

#37 - Capture GFP's use as a protein trigger

Issue - State: open - Opened by stripathy about 9 years ago

#36 - capitalization rules and matching as configuration

Issue - State: closed - Opened by stripathy over 9 years ago - 2 comments
Labels: high, easy

#35 - more permissive about missing terms that doesn't terminate the neuroNER prematurely

Issue - State: open - Opened by renaud over 9 years ago
Labels: medium, easy

#34 - issue with identifying protein names

Issue - State: closed - Opened by stripathy over 9 years ago - 2 comments
Labels: broken ruta

#33 - disambiguate multiple matches for properties

Issue - State: closed - Opened by renaud over 9 years ago

#32 - consider approaches for improving neuroNER recall

Issue - State: open - Opened by stripathy over 9 years ago
Labels: enhancement, hard

#31 - more effort to normalize brain regions

Issue - State: open - Opened by stripathy over 9 years ago - 3 comments
Labels: high, hard

#30 - layer 3/4 not correctly identified

Issue - State: closed - Opened by renaud over 9 years ago - 1 comment
Labels: wontfix, broken ruta

#29 - possible duplicate terms for layer unions

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

#28 - write more tests for neuroNER based on application to BBP/NeuroLEX cell types

Issue - State: closed - Opened by stripathy over 9 years ago - 2 comments
Labels: high

#27 - comparing neurolex to bbp and quantifying complete and partial overlap

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

#26 - Check new .obo ontologies against existing terms, like neuroLEX

Issue - State: open - Opened by stripathy over 9 years ago - 1 comment
Labels: enhancement, low

#25 - visualization idea for neuroNER neuron relationships

Issue - State: open - Opened by stripathy over 9 years ago - 1 comment
Labels: enhancement, low

#24 - weird capitalization effects for neuroNER tagging

Issue - State: closed - Opened by stripathy over 9 years ago

#23 - weird capitalization effects for neuroNER tagging

Issue - State: closed - Opened by stripathy over 9 years ago - 3 comments

#22 - check that layers and capitalization is correct

Issue - State: closed - Opened by stripathy over 9 years ago - 3 comments
Labels: wontfix, broken ruta

#21 - Remove synonyms from protein list which are too common

Issue - State: closed - Opened by stripathy over 9 years ago
Labels: high

#20 - combining EphysProp and EpyhsTrigger

Issue - State: closed - Opened by stripathy over 9 years ago - 3 comments
Labels: high, easy

#19 - Proposal for identifying ephys terms

Issue - State: closed - Opened by renaud over 9 years ago - 1 comment

#18 - add greek unicode symbols for protein synonysm

Issue - State: closed - Opened by stripathy over 9 years ago

#17 - Difficult example of listed elements with trigger words which come at end of list

Issue - State: open - Opened by stripathy over 9 years ago - 3 comments
Labels: enhancement, wontfix

#16 - add cre and Cre to protein triggers

Issue - State: closed - Opened by stripathy over 9 years ago - 1 comment
Labels: low

#15 - filter out unnecessary annotations, keep largest only

Issue - State: closed - Opened by renaud over 9 years ago
Labels: low

#14 - how does sherlok find resources?

Issue - State: closed - Opened by stripathy over 9 years ago - 1 comment

#13 - incorporate morphology ontology

Issue - State: closed - Opened by stripathy over 9 years ago

#12 - positional information

Issue - State: open - Opened by stripathy over 9 years ago
Labels: enhancement, low

#11 - Issue with identifying protein-triggers

Issue - State: closed - Opened by stripathy over 9 years ago - 3 comments
Labels: high

#10 - ensure that term isn't in different resource lists

Issue - State: open - Opened by stripathy over 9 years ago
Labels: low

#9 - abbreviation expansion is not always useful or helpful

Issue - State: open - Opened by stripathy over 9 years ago - 2 comments
Labels: enhancement, low

#8 - implement a gene name tagger and normalizer

Issue - State: open - Opened by stripathy over 9 years ago
Labels: enhancement, low

#6 - basic aggregation: fast-spiking, fast spiking, ...

Issue - State: closed - Opened by renaud over 9 years ago - 1 comment
Labels: high

#5 - gad | GAD | GAD2 should work. Too short??

Issue - State: closed - Opened by renaud over 9 years ago - 2 comments
Labels: high, broken ruta

#4 - have other people check our obo ontologies

Issue - State: open - Opened by renaud over 9 years ago - 1 comment
Labels: enhancement, low, medium

#3 - Layer as part of Brain Region

Issue - State: open - Opened by renaud over 9 years ago
Labels: low

#2 - double bouquet

Issue - State: closed - Opened by renaud over 9 years ago - 2 comments
Labels: high, broken ruta

#1 - dealing with explicitly negated statements, PV-immunonegative

Issue - State: open - Opened by stripathy over 9 years ago
Labels: enhancement, low