biopython by biopython

Official git repository for Biopython (originally converted from CVS)

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

168 -1

4,392 +7

1,759 +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

1,824 +1

509 +0

rentrez by ropensci

talk with NCBI entrez using R

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

14 +0

196 +0

38 +0

anafora by weitechen

Anafora is a web-based raw text annotation tool

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

22 +0

241 +0

54 +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

896 +5

451 +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

50 +0

12 +1

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 +0

2,608 +9

1,527 +4

HumanDiseaseOntology by DiseaseOntology

Repository for the Human Disease Ontology.

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

21 +0

347 +0

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

89 +0

20 +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

30 +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.

26 +0

177 +1

73 +1

CRAFT by UCDenver-ccp

None

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

12 +0

70 +0

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 +0

1,709 +2

228 -1

medaCy by NLPatVCU

Medical Text Mining and Information Extraction with spaCy

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

27 +0

432 +0

91 +0

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

1,954 +7

453 +1

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

667 +1

88 +0

scibert by allenai

A BERT model for scientific text.

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

52 +0

1,523 +2

217 +0