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Protocols

Argo specifications

Information


Unique identifier OMICS_05228
Name Argo
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Beta
Maintained Yes

Maintainer


  • person_outline Rafal Rak

Publications for Argo

Argo citations

 (10)
library_books

A semantic based workflow for biomedical literature annotation

2017
PMCID: 5691355
PMID: 29220478
DOI: 10.1093/database/bax088

[…] ation in the manual curation processes. With these solutions, the curation time is improved and possible mistakes from computational information extraction results are minimized. Brat (), MyMiner (), Argo () and Egas () are state-of-the-art interactive solutions, aiming to simplify the annotation process.Nonetheless, these efforts are still hindered by a lack of standardised ways to process the va […]

library_books

SciLite: a platform for displaying text mined annotations as a means to link research articles with biological data

2017
Wellcome Open Res
PMCID: 5527546
PMID: 28948232
DOI: 10.21956/wellcomeopenres.10999.r18949

[…] ls that have been developed to facilitate automated extraction of various article types and biological concepts, such as Textpresso ( ), iHOP ( ), Whatizit ( ), EAGLi ( ; ) EVEX ( ), PubTator ( ) and Argo ( ). Among these tools, Textpresso has been significantly adapted by data providers and the curation community to triage articles for curation ( ; ). Collaboration between curators and the text-m […]

library_books

Text mining resources for the life sciences

2016
PMCID: 5199186
PMID: 27888231
DOI: 10.1093/database/baw145

[…] 50 terminological resources (see ‘Useful knowledge resources’ section). The obtained corpus has been used to study the performance of named entity and event recognition techniques, implemented in the Argo workflow manager (see ‘Text mining workflow management systems’ section) using readily-available components. Finally, both the annotated corpus and the term inventory encoded in OBO format (see ‘ […]

library_books

Argo: enabling the development of bespoke workflows and services for disease annotation

2016
PMCID: 4869796
PMID: 27189607
DOI: 10.1093/database/baw066

[…] ther strategies for normalising disease mentions were explored as part of our contribution to the BioCreative V’s CDR track, described in a later section.After executing the normalisation components, Argo will prompt the user to launch the Manual Annotation Editor and supply their corrections. Once the user’s completion of his/her annotations, the annotated documents are finally saved as XMI files […]

library_books

The digital revolution in phenotyping

2015
Brief Bioinform
PMCID: 5036847
PMID: 26420780
DOI: 10.1093/bib/bbv083

[…] entities are highly relevant to phenotype acquisition. Fu et al. suggested an annotation scheme to capture phenotypes for chronic obstructive pulmonary disease in EHRs, which has been implemented in Argo [] to annotate a corpus of 1000 clinical records []. Furthermore, the newly launched DeepPhe project (http://cancer.healthnlp.org/) focusses on phenotypes relevant in the cancer genomics domain.U […]

call_split

Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013

2015
BMC Bioinformatics
PMCID: 4511510
PMID: 26202570
DOI: 10.1186/1471-2105-16-S10-S2
call_split See protocol

[…] as applied for the CG task ORGANISM mentions. The overall processing used the pipeline first introduced for similar analysis for the BioNLP ST'11 []. These tools were additionally integrated into the Argo workflow system [] to support the PC task curation process. Following initial automatic entity mention annotation, we performed manual revision of the outputs to correct tagger errors prior to ad […]

Citations

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Argo institution(s)
National Centre for Text Mining, School of Computer Science, University of Manchester, UK; Department of Computer Science, University of the Philippines Diliman, Philippines

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