NCATSTranslator Text-Mining-Provider-Roadmap issues

NCATSTranslator / Text-Mining-Provider-Roadmap

Roadmap and issue tracking for the NCATS Translator Text Mining Provider

MIT License

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Benchmark different BERT models for the Biolink association extraction tasks

#47 bill-baumgartner opened 3 years ago
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Develop concept recognition system that targets taxon-specific protein mentions

#46 bill-baumgartner opened 3 years ago
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Operationalize results of Lee et al. 2017 system error analysis

#45 bill-baumgartner opened 3 years ago
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Error analysis of Lee et al. 2017 coreference system output

#44 bill-baumgartner opened 3 years ago
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Retrain & evaluate the Lee et al. 2017 system on the CRAFT corpus

#43 bill-baumgartner opened 3 years ago
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Incorporate evaluation of relation classification BERT models into CI/CD

#42 bill-baumgartner opened 3 years ago
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Incorporate benchmarking of concept recognition OGER components into CI/CD

#41 bill-baumgartner opened 3 years ago
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Incorporate benchmarking of concept recognition CRF components into CI/CD

#40 bill-baumgartner opened 3 years ago
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Incorporate BLUE benchmark relation evaluation code to the benchmarking system

#39 bill-baumgartner opened 3 years ago
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Add data/code to evaluate MONDO concept recognition to the benchmarking system

#38 bill-baumgartner opened 3 years ago
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Add data/code to evaluate HPO concept recognition to the benchmarking system

#37 bill-baumgartner opened 3 years ago
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Develop a text-mining error feedback collection system

#36 bill-baumgartner opened 3 years ago
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Implement error-reporting system

#35 bill-baumgartner closed 3 years ago
1
Design error-reporting system

#34 bill-baumgartner opened 3 years ago
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Reach out to Translator community to see if others are designing feedback collection systems

#33 bill-baumgartner opened 3 years ago
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Define requirements for a text-mining error-reporting system

#32 bill-baumgartner opened 3 years ago
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Develop relation annotation tool

#31 bill-baumgartner opened 3 years ago
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Investigate existing annotation tools; evaluate against requirements

#30 bill-baumgartner opened 3 years ago
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Define requirements for relation annotation tool

#29 bill-baumgartner opened 3 years ago
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Select six new Biolink associations to target for extraction via text-mining

#28 bill-baumgartner opened 3 years ago
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Create patterns mapping CRAFT assertions to biolink:GeneToExpressionSiteLocationAssociation

#27 bill-baumgartner opened 3 years ago
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Find appropriate Biolink relation for has_symptom

#26 bill-baumgartner opened 3 years ago
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Create patterns mapping CRAFT assertions to biolink:DiseaseToPhenotypicFeatureAssociation

#25 bill-baumgartner opened 3 years ago
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Create patterns mapping CRAFT assertions to biolink:GeneToDiseaseAssociation

#24 bill-baumgartner opened 3 years ago
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Create patterns mapping CRAFT assertions to biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation

#23 bill-baumgartner opened 3 years ago
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Create patterns mapping CRAFT assertions to biolink:GeneRegulatoryRelationshipAssociation

#22 bill-baumgartner opened 3 years ago
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Create patterns mapping CRAFT assertions to biolink:ChemicalToGeneAssociation

#21 bill-baumgartner opened 3 years ago
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Complete annotation of CRAFT with MONDO

#20 bill-baumgartner opened 3 years ago
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Complete annotation of CRAFT with Mammalian Phenotype Ontology

#19 bill-baumgartner opened 3 years ago
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Explore extension of uPheno with generic phenotype classes

#18 bill-baumgartner opened 3 years ago
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Explore BO-LSTM tool for classifying relationships between ontology concepts

#17 bill-baumgartner opened 4 years ago
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add READMEs for KG types

#16 bill-baumgartner closed 4 years ago
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Integrate disambiguated author names into document metadata

#15 bill-baumgartner opened 4 years ago
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Add behavioral testing of NLP models with CheckList to the NLP evaluation platform

#14 bill-baumgartner opened 4 years ago
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add sample text-mined KG v0.1

#13 bill-baumgartner closed 4 years ago
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Create sample text-mined KG in KGX TSV format based on the CRAFT corpus

#12 bill-baumgartner closed 4 years ago
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Develop a prioritization scheme for reprocessing documents due to ontology/software updates

#11 bill-baumgartner opened 4 years ago
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Benchmarking script access

#10 southalln opened 4 years ago
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New association type request -- gene to disease association

#9 bill-baumgartner opened 4 years ago
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New association type request -- chemical treats disease

#8 bill-baumgartner opened 4 years ago
1
New association type request -- gene regulates gene

#7 bill-baumgartner opened 4 years ago
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New association type request -- chemical regulates gene

#6 bill-baumgartner opened 4 years ago
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Explore methods to speed up prediction using BERT models

#5 bill-baumgartner opened 4 years ago
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Balance concept recognition performance with document throughput using CRFs

#4 bill-baumgartner closed 3 years ago
1
Add concepts from the Monarch disease ontology (Mondo)

#3 bill-baumgartner opened 4 years ago
0
Add concepts from the Human Phenotype Ontology

#2 bill-baumgartner opened 4 years ago
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Add issue templates for this repository

#1 bill-baumgartner closed 4 years ago
1