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

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

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

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

BioGPT by Microsoft

None

created at Aug. 15, 2022, 5:55 a.m.

71 +0

4,307 +6

452 +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

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

scibert by allenai

A BERT model for scientific text.

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

52 +0

1,523 +2

217 +0

clinicalBERT by EmilyAlsentzer

repository for Publicly Available Clinical BERT Embeddings

created at April 5, 2019, 8:50 p.m.

25 +0

674 +1

135 +0

HumanDiseaseOntology by DiseaseOntology

Repository for the Human Disease Ontology.

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

21 +0

347 +0

108 -1

clinicalBERT by kexinhuang12345

ClinicalBERT: Modeling Clinical Notes and Predicting Hospital Readmission (CHIL 2020 Workshop)

created at March 30, 2019, 8:06 a.m.

14 +0

381 +1

98 +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-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

bluebert by ncbi-nlp

BlueBERT, pre-trained on PubMed abstracts and clinical notes (MIMIC-III).

created at June 6, 2019, 2:02 p.m.

23 +0

558 +0

78 +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

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

rentrez by ropensci

talk with NCBI entrez using R

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

14 +0

196 +0

38 +0

BioWordVec by ncbi-nlp

None

created at Feb. 22, 2019, 4:32 p.m.

11 +0

144 +0

29 +0

med7 by kormilitzin

None

created at Feb. 26, 2020, 11:03 p.m.

13 +0

205 +0

26 +1

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