Text-mining-assisted biocuration workflows in Argo by Rafal Rak, et al. (Database (2014) 2014 : bau070 doi: 10.1093/database/bau070)
Abstract:
Biocuration activities have been broadly categorized into the selection of relevant documents, the annotation of biological concepts of interest and identification of interactions between the concepts. Text mining has been shown to have a potential to significantly reduce the effort of biocurators in all the three activities, and various semi-automatic methodologies have been integrated into curation pipelines to support them. We investigate the suitability of Argo, a workbench for building text-mining solutions with the use of a rich graphical user interface, for the process of biocuration. Central to Argo are customizable workflows that users compose by arranging available elementary analytics to form task-specific processing units. A built-in manual annotation editor is the single most used biocuration tool of the workbench, as it allows users to create annotations directly in text, as well as modify or delete annotations created by automatic processing components. Apart from syntactic and semantic analytics, the ever-growing library of components includes several data readers and consumers that support well-established as well as emerging data interchange formats such as XMI, RDF and BioC, which facilitate the interoperability of Argo with other platforms or resources. To validate the suitability of Argo for curation activities, we participated in the BioCreative IV challenge whose purpose was to evaluate Web-based systems addressing user-defined biocuration tasks. Argo proved to have the edge over other systems in terms of flexibility of defining biocuration tasks. As expected, the versatility of the workbench inevitably lengthened the time the curators spent on learning the system before taking on the task, which may have affected the usability of Argo. The participation in the challenge gave us an opportunity to gather valuable feedback and identify areas of improvement, some of which have already been introduced.
Database URL: http://argo.nactem.ac.uk
From the introduction:
Data curation from biomedical literature had been traditionally carried out as an entirely manual effort, in which a curator handpicks relevant documents and creates annotations for elements of interest from scratch. To increase the efficiency of this task, text-mining methodologies have been integrated into curation pipelines. In curating the Biomolecular Interaction Network Database (1), a protein–protein interaction extraction system was used and was shown to be effective in reducing the curation work-load by 70% (2). Similarly, a usability study revealed that the time needed to curate FlyBase records (3) was reduced by 20% with the use of a gene mention recognizer (4). Textpresso (5), a text-mining tool that marks up biomedical entities of interest, was used to semi-automatically curate mentions of Caenorhabditis elegans proteins from the literature and brought about an 8-fold increase in curation efficiency (6). More recently, the series of BioCreative workshops (http://www.biocreative.org) have fostered the synergy between biocuration efforts and text-mining solutions. The user-interactive track of the latest workshop saw nine Web-based systems featuring rich graphical user interfaces designed to perform text-mining-assisted biocuration tasks. The tasks can be broadly categorized into the selection of documents for curation, the annotation of mentions of relevant biological entities in text and the annotation of interactions between biological entities (7).
Argo is a truly impressive text-mining-assisted biocuration application but the first line of a biocuration article needs to read:
Data curation from biomedical literature had been traditionally carried out as an entirely ad-hoc effort, after the author has submitted their paper for publication.
There is an enormous backlog of material that desperately needs biocuration and Argo (and other systems) have a vital role to play in that effort.
However, the situation of ad-hoc biocuration is never going to improve unless and until biocuration is addressed in the authoring of papers to appear in biomedical literature.
Who better to answer questions or ambiguities that appear in biocuration than the author of papers?
That would require working to extend MS Office and Apache OpenOffice, to name two of the more common authoring platforms.
But the return would be higher quality publications earlier in the publication cycle, which would enable publishers to provide enhanced services based upon higher quality products and enhance tracing and searching of the end products.
No offense to ad-hoc efforts but higher quality sooner in the publication process seems like an unbeatable deal.