biopython by biopython

Official git repository for Biopython (originally converted from CVS)

created at March 15, 2009, 9:09 p.m.

168 -2

4,175 +6

1,714 +2

brat by nlplab

brat rapid annotation tool (brat) - for all your textual annotation needs

created at Jan. 28, 2011, 5:37 a.m.

80 +0

1,776 +1

510 -1

rentrez by ropensci

talk with NCBI entrez using R

created at Feb. 11, 2012, 11:44 p.m.

14 +0

190 -1

40 +0

anafora by weitechen

Anafora is a web-based raw text annotation tool

created at April 8, 2013, 4:44 p.m.

22 +0

238 +0

55 +0

CommonDataModel by OHDSI

Definition and DDLs for the OMOP Common Data Model (CDM)

created at Oct. 14, 2014, 8:20 p.m.

124 +0

832 +2

437 +0

ctakes by apache

Apache cTAKES is a Natural Language Processing (NLP) platform for clinical text.

created at Nov. 21, 2014, 8 a.m.

12 +0

36 +0

9 +0

mimic-code by MIT-LCP

MIMIC Code Repository: Code shared by the research community for the MIMIC family of databases

created at Sept. 1, 2015, 11:03 p.m.

135 +1

2,327 +5

1,481 +3

HumanDiseaseOntology by DiseaseOntology

Repository for the Human Disease Ontology.

created at Sept. 23, 2015, 2:48 p.m.

20 +0

323 +1

108 +1

Bio-SCoRes by kilicogluh

A smorgasbord architecture for coreference resolution in biomedical text

created at Feb. 12, 2016, 6:57 p.m.

6 +0

9 +0

1 +0

TabInOut by nikolamilosevic86

Framework for information extraction from tables

created at April 7, 2016, 3:41 p.m.

5 +0

41 +0

10 +0

CogStack-SemEHR by CogStack

Surfacing Semantic Data from Clinical Notes in Electronic Health Records for Tailored Care, Trial Recruitment and Clinical Research

created at Oct. 14, 2016, 10:21 a.m.

25 +0

86 +0

19 +0

pubrunner by jakelever

A framework for keeping biomedical text mining result up-to-date

created at Aug. 30, 2017, 9:30 p.m.

7 +0

41 +0

6 +0

DeepPhe-Release by DeepPhe

Public release of the DeepPhe analytic software

created at Oct. 2, 2017, 4:27 p.m.

12 +0

29 +0

10 +0

biolink-model by biolink

Schema and generated objects for biolink data model and upper ontology

created at Dec. 4, 2017, 4:45 a.m.

23 +0

167 +2

71 +0

CRAFT by UCDenver-ccp

None

created at April 30, 2018, 10:17 p.m.

12 +0

67 +1

15 +0

scispacy by allenai

A full spaCy pipeline and models for scientific/biomedical documents.

created at Sept. 24, 2018, 9:45 p.m.

52 -1

1,617 +2

221 +0

medaCy by NLPatVCU

Medical Text Mining and Information Extraction with spaCy

created at Sept. 28, 2018, 2:48 p.m.

26 +0

423 +2

91 -1

biobert by dmis-lab

Bioinformatics'2020: BioBERT: a pre-trained biomedical language representation model for biomedical text mining

created at Jan. 24, 2019, 6:27 p.m.

62 +0

1,845 +3

439 +0

biobert-pretrained by naver

BioBERT: a pre-trained biomedical language representation model for biomedical text mining

created at Jan. 28, 2019, 2:05 a.m.

26 +0

631 +1

85 +0

scibert by allenai

A BERT model for scientific text.

created at Jan. 30, 2019, 7 p.m.

50 +0

1,438 +6

211 +0