Text-mining-assisted biocuration workflows in Argo

Rak, Rafał; Batista-Navarro, Riza Theresa; Rowley, Andrew; Carter, Jacob; Ananiadou, Sophia

doi:10.1093/database/bau070

Cited by 21 publications

(14 citation statements)

References 38 publications

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“…Some development of tools beyond the scope of a single project already started, addressing the large amount of text mining done by biocurators (W ei et al . 2013; R ak et al . 2014; S inghal et al .…”

Section: Supplemental Materialsmentioning

confidence: 99%

FlyClockbase: Importance of Biological Model Curation for Analyzing Variability in the Circadian Clock of Drosophila melanogaster by Integrating Time Series from 25 Years of Research

Scheuer

Hanlon

Dresel

et al. 2017

Preprint

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General Article SummarySubstantial biological model curation was essential for identifying differences in peak 23 time variance of the clock-proteins 'PERIOD' and 'TIMELESS', which probably stem 24 from differences in phosphorylation-network complexity. 25 We repeatedly encountered systemic limitations of contemporary data analysis 26 strategies in our work on circadian clocks. Thus, we used it as an opportunity for 27 composing a panoramic view of the broader challenges in biological model curation, 28 which are likely to increase as biologists aim to integrate all existing expertise in order to 29 address diverse grand challenges. We developed and tested a trans-disciplinary 30 research workflow, which enables biologists and compiler-architects to define biology-31 friendly compilers for efficiently constructing and maintaining Versioned Biological 32 Information Resources (VBIRs). We report insights gleaned from our practical clock 33 research that are essential for defining a VBIRs infrastructure, which improves the 34 efficiency of biological model curation to the point where it can be democratized. . CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/099192 doi: bioRxiv preprint first posted online Jan. 9, 2017;. CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/099192 doi: bioRxiv preprint first posted online Jan. 9, 2017;. CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/099192 doi: bioRxiv preprint first posted online Jan. 9, 2017;. CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/099192 doi: bioRxiv preprint first posted online Jan. 9, 2017;. CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/099192 doi: bioRxiv preprint first posted online Jan. 9, 2017;. CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/099192 doi: bioRxiv preprint first posted online Jan. 9, 2017;. CC-BY 4.0 International license It ...

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Section: Supplemental Materialsmentioning

confidence: 99%

FlyClockbase: Importance of Biological Model Curation for Analyzing Variability in the Circadian Clock of Drosophila melanogaster by Integrating Time Series from 25 Years of Research

Scheuer

Hanlon

Dresel

et al. 2017

Preprint

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“…The vision of Argo is to create an easy to use but highly functional WMS for the life-sciences community and beyond to engage in a variety of tasks around text mining, including biocuration (82). It provides a powerful mechanism to obtain and process multiple documents in a user-friendly environment.…”

Section: Tools and Servicesmentioning

confidence: 99%

“…It provides a powerful mechanism to obtain and process multiple documents in a user-friendly environment. A variety of export options are available to obtain the final results of processing, including type systems tailored to a particular application (83) and web services supporting interoperable formats (84). Argo is accessible and usable via the web, where a large collection of ready-to-use components can be combined by a novice user to build a workflow.…”

Section: Tools and Servicesmentioning

confidence: 99%

Text mining resources for the life sciences

Przybyła¹,

Shardlow²,

Aubin³

et al. 2016

Database

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Text mining is a powerful technology for quickly distilling key information from vast quantities of biomedical literature. However, to harness this power the researcher must be well versed in the availability, suitability, adaptability, interoperability and comparative accuracy of current text mining resources. In this survey, we give an overview of the text mining resources that exist in the life sciences to help researchers, especially those employed in biocuration, to engage with text mining in their own work. We categorize the various resources under three sections: Content Discovery looks at where and how to find biomedical publications for text mining; Knowledge Encoding describes the formats used to represent the different levels of information associated with content that enable text mining, including those formats used to carry such information between processes; Tools and Services gives an overview of workflow management systems that can be used to rapidly configure and compare domain- and task-specific processes, via access to a wide range of pre-built tools. We also provide links to relevant repositories in each section to enable the reader to find resources relevant to their own area of interest. Throughout this work we give a special focus to resources that are interoperable—those that have the crucial ability to share information, enabling smooth integration and reusability.

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“…To this end, Europe PMC aspires to provide text and data miners with the means to publish the outcomes of their algorithms in the context of articles in Europe PMC. This is exemplified by the Evidence Finder application, which is invoked on the full-text search for queries based on gene/protein names, diseases, organisms, chemicals and anatomical entities ( 14 ), extracted using the text mining workbench Argo ( 15 , 16 ). Evidence Finder shows facts or claims, together with their interpretations ( 17 ), hidden in full-text articles based on the user's query, displaying relevant text fragments alongside the article metadata on search results lists on Europe PMC Labs.…”

Section: Europe Pmc Resources For Text and Data Minersmentioning

confidence: 99%

Europe PMC: a full-text literature database for the life sciences and platform for innovation

2014

Nucleic Acids Research

113

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This article describes recent developments of Europe PMC (http://europepmc.org), the leading database for life science literature. Formerly known as UKPMC, the service was rebranded in November 2012 as Europe PMC to reflect the scope of the funding agencies that support it. Several new developments have enriched Europe PMC considerably since then. Europe PMC now offers RESTful web services to access both articles and grants, powerful search tools such as citation-count sort order and data citation features, a service to add publications to your ORCID, a variety of export formats, and an External Links service that enables any related resource to be linked from Europe PMC content.

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Text-mining-assisted biocuration workflows in Argo

Cited by 21 publications

References 38 publications

FlyClockbase: Importance of Biological Model Curation for Analyzing Variability in the Circadian Clock of Drosophila melanogaster by Integrating Time Series from 25 Years of Research

FlyClockbase: Importance of Biological Model Curation for Analyzing Variability in the Circadian Clock of Drosophila melanogaster by Integrating Time Series from 25 Years of Research

Text mining resources for the life sciences

Europe PMC: a full-text literature database for the life sciences and platform for innovation

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