Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: Brat

https://packages.ecosyste.ms/registries/pypi.org/packages/Brat

Simple framework for creating REST APIs
1 version
Latest release: almost 11 years ago
21 downloads last month

Papers Mentioning Brat 20

Natural language processing of radiology reports for the detection of thromboembolic diseases and clinically relevant incidental findings
Cited by: 80
Author(s): Anne-Dominique Pham, Aurélie Névéol, Thomas Lee, D Yasunaga, Olivier Clémеnt, Guy Meyer, Rémy Morello, Anita Burgun
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0226176

Menagerie: A text-mining tool to support animal-human translation in neurodegeneration research
Cited by: 9
Author(s): Caroline J. Zeiss, Dongwook Shin, Brent Vander Wyk, Amanda P. Beck, Natalie Zatz, Charles Sneiderman, Halil Kilicoglu
Software Mentions: 2
Published: almost 5 years ago

10.1093/database/bau048

Egas: a collaborative and interactive document curation platform
Cited by: 21
Author(s): David Campos, Jóni Lourenço, Sérgio Matos, José Luís Oliveira
Software Mentions: 2
Published: over 10 years ago

10.1093/database/baw096

Mining clinical attributes of genomic variants through assisted literature curation in Egas
Cited by: 6
Author(s): Sérgio Matos, David Campos, Renato P. Pinho, Raquel M. Silva, Matthew Mort, David Neil Cooper, José Luís Oliveira
Software Mentions: 2
Published: almost 9 years ago

10.1093/database/bax088

A semantic-based workflow for biomedical literature annotation
Cited by: 1
Author(s): Pedro Sernadela, José Luís Oliveira
Software Mentions: 2
Published: almost 8 years ago

10.3389/fnbeh.2017.00124

Functional Connectivity Differences in the Insular Sub-regions in Migraine without Aura: A Resting-State Functional Magnetic Resonance Imaging Study
Cited by: 16
Author(s): Zhaojie Yu, Yan-bing Lv, Lingheng Song, Daihong Liu, Xueling Huang, Xinyue Hu, Zhiwei Zuo, Yao Wang, Qian Yang, Jing Peng, Zhenhua Zhou, Haitao Li
Software Mentions: 2
Published: over 7 years ago

10.3389/fmed.2019.00066

The Revival of the Notes Field: Leveraging the Unstructured Content in Electronic Health Records
Cited by: 50
Author(s): Michela Assale, Linda Greta Dui, Andrea Cina, Andrea Seveso, Federico Cabitza
Software Mentions: 2
Published: over 5 years ago

10.1038/sdata.2018.1

A dataset of 200 structured product labels annotated for adverse drug reactions
Cited by: 38
Author(s): Dina Demner‐Fushman, Sonya E. Shooshan, Laritza Rodriguez, Alan R. Aronson, F.M. Lang, Willie J. Rogers, Kirk Roberts, Joseph M. Tonning
Software Mentions: 2
Published: almost 7 years ago

10.1186/s40035-015-0027-z

Voxel-based meta-analysis of grey matter changes in Alzheimer’s disease
Cited by: 81
Author(s): Wenying Wang, Jin‐Tai Yu, Yong Liu, Ruihua Yin, Hui-Fu Wang, Jun Wang, Lin Tan, Joaquim Radúa, Lan Tan
Software Mentions: 2
Published: over 9 years ago

10.2196/13914

A Systematic Framework for Analyzing Patient-Generated Narrative Data: Protocol for a Content Analysis
Cited by: 9
Author(s): Maryam Zolnoori, Joyce E. Balls-Berry, Tabetha A. Brockman, Christi A. Patten, Ming Huang, Lixia Yao
Software Mentions: 2
Published: about 5 years ago

10.3389/fnagi.2016.00064

Voxel-Wise Meta-Analysis of Gray Matter Changes in Amyotrophic Lateral Sclerosis
Cited by: 45
Author(s): Dongchao Shen, Liying Cui, Fang Jia, Bo Cui, Dawei Li, Hongfei Tai
Software Mentions: 1
Published: over 8 years ago

10.1186/s12911-019-0908-7

A validated natural language processing algorithm for brain imaging phenotypes from radiology reports in UK electronic health records
Cited by: 26
Author(s): Emily Wheater, Grant Mair, Cathie Sudlow, Beatrice Alex, Claire Grover, William Whiteley
Software Mentions: 1
Published: about 5 years ago

10.2196/publichealth.6396

TwiMed: Twitter and PubMed Comparable Corpus of Drugs, Diseases, Symptoms, and Their Relations
Cited by: 55
Author(s): Nestor Alvaro, Yusuke Miyao, Nigel Collier
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0221582

A corpus of plant–disease relations in the biomedical domain
Cited by: 6
Author(s): Baeksoo Kim, Wonjun Choi, Hyunju Lee
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0107477

Annotated Chemical Patent Corpus: A Gold Standard for Text Mining
Cited by: 54
Author(s): Saber A. Akhondi, Alexander Klenner, Christian Tyrchan, Anil K. Manchala, Kiran Boppana, Daniel M. Lowe, Marc Zimmermann, Sarma A.R.P. Jagarlapudi, Roger A. Sayle, Jan A. Kors, Sorel Mureşan
Software Mentions: 1
Published: about 10 years ago

10.1093/database/baw090

MET network in PubMed: a text-mined network visualization and curation system
Cited by: 6
Author(s): Hong-Jie Dai, Chu Hsien Su, Po Ting Lai, Ming Huang, Jitendra Jonnagaddala, Toni Rose Jue, Shruti Rao, Hui Jou Chou, Marija Milacic, Onkar Singh, Shabbir Syed-Abdul, Wen Lian Hsu
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41597-020-00620-0

Chia, a large annotated corpus of clinical trial eligibility criteria
Cited by: 17
Author(s): Fabrício S. P. Kury, Alex Butler, Chi Yuan, Li-heng Fu, Yingcheng Sun, Hao Líu, Ida Sim, Simona Carini, Chunhua Weng
Software Mentions: 1
Published: about 4 years ago

10.1186/s13326-021-00244-2

Synthetic data for annotation and extraction of family history information from clinical text
Cited by: 5
Author(s): P. Brekke, Taraka Rama, Ildikó Pilán, Øystein Nytrø, Lilja Øvrelid
Software Mentions: 1
Published: over 3 years ago

10.1186/1758-2946-7-S1-S2

The CHEMDNER corpus of chemicals and drugs and its annotation principles
Cited by: 198
Author(s): Martin Krallinger, Obdulia Rabal, Florian Leitner, Miguél Vázquez, David Salgado, Zhiyong Lu, Robert Leaman, Yanan Lu, Donghong Ji, Daniel M. Lowe, Roger A. Sayle, Riza Theresa Batista-Navarro, Rafał Rak, Torsten Huber, Tim Rocktäschel, Sérgio Matos, David Campos, Buzhou Tang, Hua Xu, Tsendsuren Munkhdalai, Keun Ho Ryu, S. V. Ramanan, Senthil Nathan, Slavko Žitnik, Marko Bajec, Lutz Weber, Matthias Irmer, Saber A. Akhondi, Jan A. Kors, Shuo Xu, Xueli An, Utpal Kumar Sikdar, Asif Ekbal, Masaharu Yoshioka, Thaer M. Dieb, Miji Choi, Karin Verspoor, Madian Khabsa, C. Lee Giles, Hongfang Liu, K. E. Ravikumar, André Lamúrias, Francisco M. Couto, Hong Jie Dai, Richard Tzong-Han Tsai, Caglar Ata, Tolga Can, Anabel Usié, Rui Alves, Isabel Segura-Bedmar, Paloma Martı́nez, Julen Oyarzábal, Alfonso Valencia
Software Mentions: 1
Published: almost 10 years ago

10.12688/f1000research.3216.1

An analysis on the entity annotations in biological corpora
Cited by: 19
Author(s): Mariana Neves
Software Mentions: 1
Published: over 10 years ago