renaud neuroNER issues - Githubissues

renaud / neuroNER

named entity recognizer for neuronal cells, based on UIMA Ruta rules

GNU Lesser General Public License v3.0

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issues

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SEVERE: Can't find bluima/neuroner

#64 sepehrgolriz opened 4 years ago
0
Add cells from regenbase ontology

#63 stripathy opened 8 years ago
0
Plan for ontologizing neuroNER

#62 dosumis opened 8 years ago
10
Pypi updates

#61 stripathy opened 8 years ago
0
get DB crossrefs for UBERON term

#60 stripathy closed 8 years ago
2
export uberon structure name as exact synonym .obo file

#59 stripathy closed 8 years ago
4
updates to obo resource files breaks sherlok parsing

#58 stripathy opened 8 years ago
2
variants of allen brain regions

#57 tgbugs opened 8 years ago
14
switch ontology resource backend to .ttl from .obo

#56 stripathy opened 8 years ago
1
lower number of UNKN brain regions

#55 renaud opened 8 years ago
0
migrate to UBERON for brain regions and synonyms

#54 stripathy opened 8 years ago
16
create an alpha release of neuroNER and put on pip

#53 stripathy opened 8 years ago
5
consider using neuroelectro to show neuroNER queries

#52 stripathy opened 8 years ago
2
benchmark neuroNER coverage against existing ontologies

#51 stripathy opened 8 years ago
2
improve synonyms for brain regions

#50 stripathy opened 8 years ago
0
cleanup of obo files

#49 tgbugs closed 8 years ago
1
Leverage the work done in OBO community to build interoperable ontologies

#48 cmungall opened 8 years ago
12
NBC wrongly recognized as protein

#47 renaud closed 8 years ago
0
update similarity rules for layers to better capture is_a relationships

#46 stripathy closed 8 years ago
0
resolve discrepancy between Isocortex, and cerebral cortex in ABA ontology

#45 stripathy opened 8 years ago
0
only keep a single ontology term corresponding to the same span of text

#44 stripathy closed 8 years ago
1
consider giving short names to ontology terms, then cause use normalization for term shortening

#43 stripathy closed 8 years ago
0
traverse layer ontology and return major parts along with subparts

#42 stripathy closed 8 years ago
0
return ABA major brain region along with found sub regions

#41 stripathy closed 8 years ago
0
Adding regions_lfrench.mappings.csv

#40 leonfrench opened 8 years ago
0
why is layer not being found here?

#39 stripathy closed 8 years ago
1
Encode the various ways of encoding a hyphen sign

#38 stripathy opened 8 years ago
0
Capture GFP's use as a protein trigger

#37 stripathy opened 8 years ago
0
capitalization rules and matching as configuration

#36 stripathy closed 8 years ago
2
more permissive about missing terms that doesn't terminate the neuroNER prematurely

#35 renaud opened 8 years ago
0
issue with identifying protein names

#34 stripathy closed 8 years ago
2
disambiguate multiple matches for properties

#33 renaud closed 8 years ago
0
consider approaches for improving neuroNER recall

#32 stripathy opened 8 years ago
0
more effort to normalize brain regions

#31 stripathy opened 8 years ago
3
layer 3/4 not correctly identified

#30 renaud closed 8 years ago
1
possible duplicate terms for layer unions

#29 stripathy closed 8 years ago
2
write more tests for neuroNER based on application to BBP/NeuroLEX cell types

#28 stripathy closed 8 years ago
2
comparing neurolex to bbp and quantifying complete and partial overlap

#27 stripathy closed 8 years ago
2
Check new .obo ontologies against existing terms, like neuroLEX

#26 stripathy opened 8 years ago
1
visualization idea for neuroNER neuron relationships

#25 stripathy opened 8 years ago
1
weird capitalization effects for neuroNER tagging

#24 stripathy closed 8 years ago
0
weird capitalization effects for neuroNER tagging

#23 stripathy closed 8 years ago
3
check that layers and capitalization is correct

#22 stripathy closed 8 years ago
3
Remove synonyms from protein list which are too common

#21 stripathy closed 8 years ago
0
combining EphysProp and EpyhsTrigger

#20 stripathy closed 8 years ago
3
Proposal for identifying ephys terms

#19 renaud closed 8 years ago
1
add greek unicode symbols for protein synonysm

#18 stripathy closed 9 years ago
0
Difficult example of listed elements with trigger words which come at end of list

#17 stripathy opened 9 years ago
3
add cre and Cre to protein triggers

#16 stripathy closed 9 years ago
1
filter out unnecessary annotations, keep largest only

#15 renaud closed 8 years ago
0