- Open Access
Toward an interactive article: integrating journals and biological databases
© Rangarajan et al; licensee BioMed Central Ltd. 2011
- Received: 13 August 2010
- Accepted: 19 May 2011
- Published: 19 May 2011
Journal articles and databases are two major modes of communication in the biological sciences, and thus integrating these critical resources is of urgent importance to increase the pace of discovery. Projects focused on bridging the gap between journals and databases have been on the rise over the last five years and have resulted in the development of automated tools that can recognize entities within a document and link those entities to a relevant database. Unfortunately, automated tools cannot resolve ambiguities that arise from one term being used to signify entities that are quite distinct from one another. Instead, resolving these ambiguities requires some manual oversight. Finding the right balance between the speed and portability of automation and the accuracy and flexibility of manual effort is a crucial goal to making text markup a successful venture.
We have established a journal article mark-up pipeline that links GENETICS journal articles and the model organism database (MOD) WormBase. This pipeline uses a lexicon built with entities from the database as a first step. The entity markup pipeline results in links from over nine classes of objects including genes, proteins, alleles, phenotypes and anatomical terms. New entities and ambiguities are discovered and resolved by a database curator through a manual quality control (QC) step, along with help from authors via a web form that is provided to them by the journal. New entities discovered through this pipeline are immediately sent to an appropriate curator at the database. Ambiguous entities that do not automatically resolve to one link are resolved by hand ensuring an accurate link. This pipeline has been extended to other databases, namely Saccharomyces Genome Database (SGD) and FlyBase, and has been implemented in marking up a paper with links to multiple databases.
Our semi-automated pipeline hyperlinks articles published in GENETICS to model organism databases such as WormBase. Our pipeline results in interactive articles that are data rich with high accuracy. The use of a manual quality control step sets this pipeline apart from other hyperlinking tools and results in benefits to authors, journals, readers and databases.
- Automate Tool
- Entity Class
- Saccharomyces Genome Database
- Quality Control Step
- Model Organism Database
The development of linking tools using automatic entity recognition is an active area of research. One such recent tool is Reflect. Reflect identifies and highlights gene names, protein names and small molecules. When a user clicks on a highlighted entity in a Reflect-processed article, a pop-up window displays relevant information about the entity mined from a core source of databases. Reflect can be invoked from within a web browser by the use of a browser plug-in making this hyperlinking tool quite portable, and as a fully automated hyperlinking tool, it is fast. However, the downside of being fully automated is that it might lack accuracy and depth.
Automated tools have become excellent at identifying entities that exist in a database, but are necessarily limited in accuracy to those entities that are unique i.e., they are not ambiguous within or across databases. Further, since automated tools only identify entities that already exist in a database, they miss the most relevant information in a research paper - the entity that has been discovered but has yet to be entered into a database. Finally, several of these tools are limited in scope to a minimum number of entity types e.g., genes, proteins, or chemicals; whereas understanding the science in a research paper often requires a reader to understand more about the research system in which these genes and proteins are assayed and concluded to work. Such information, if not presented in the paper leaves novice scientists and scientists outside of the field of study at the mercy of the authors' writing ability and journal-imposed word limits; and whereas this information, such as species specific anatomy and phenotypes are available in databases, access to the relevant pages in the database may not be inherently obvious to the non-initiated database user.
Here we describe a pipeline by which interactive full-text HTML/PDF journal articles are published with named entities in articles linked to corresponding resource pages in biological databases. Such interactive articles allow a reader to click on a gene, protein, transgene, or potentially any object found in the database, and direct the reader to the relevant webpage. This seamless connection from the article to summaries of single-dimensional and high-dimensional data types promotes a deeper level of understanding for the naïve reader and incisive evaluation for the sophisticated reader. Furthermore, this immediate connection to primary data advances planning and conducting the next generation of investigations. Finally, ongoing curation at the biological database ensures that linked content evolves with the field. This linking has already proved successful in the result pages of the Textpresso search engine , developed by some of the authors of this paper .
The linking pipeline explained in this article has been established for articles discussing the model organism Caenorhabditis elegans (C. elegans) published in the journal GENETICS. The databases used for this project are WormBase  for linking C. elegans articles and Saccharomyces Genome Database (SGD)  for linking Saccharomyces cerevisiae (S. cerevisiae) articles. Further, a pipeline is under construction with Flybase  for linking Drosophila melanogaster (D. melanogaster) articles.
Journal and journal services
In 2009, editors of the journal GENETICS  approached WormBase to provide linking from C. elegans articles to WormBase. GENETICS articles are processed by Dartmouth Journal Services (DJS). DJS provides XML formatted files for linking through a web service to WormBase. After linked files undergo a manual quality control step at WormBase, the linked file is returned to DJS. DJS processes the linked file creating a linked PDF, which is sent back to WormBase for final approval and then to the author for a final proof. If mistakes are found during the PDF proof stage they are fixed by DJS. Questions concerning ambiguities and formatting errors that arise during the quality control step at the database are relayed to the author through DJS.
If any new objects declared through the author form are not in WormBase at the time of linking, the links for the new, author-declared entities are silent when they are inserted into the article (prior to actual publication). The author form also alerts WormBase curators to the presence of these new entities, which will then be added to the next release of the database by the curator. Links to these new entities are usually live when the article is published or soon thereafter.
Examples of WormBase links inserted in C. elegans articles
For S. cerevisiae yeast articles, SGD provides gene, protein, and variation entity lists. The URL pattern used is http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=SGDID, where SGDID is the SGD identification for the entity.
For D. melanogaster articles, FlyBase provides entities from five different classes: genes, alleles, aberrations, transgenic transposons and transposon insertions. The URL pattern used is http://flybase.org/reports/FBID.html, where FBID is the FlyBase identification for the entity. FlyBase suffers from the unique problem of having several common English words (for example: for, we, a) as gene names. Since we receive XML formatted files from the journal publisher, the policy is to link an entity only if it is italicized i.e. within italic tags in the XML.
After the paper has gone through the automated linking script, a link to the marked up paper is sent to the database curator for a manual quality control (QC) step to ensure all appropriate links are made. QC curators use an html viewer to manually assess each link for accuracy. The curator also searches the paper to make sure any new entity has been identified and linked. Additions, deletions and any corrections to the links in the XML file are done using a text editor or an XML editor.
Ensuring stable URLs
An important requirement for this project is long-term stability of the database URLs. The databases need to be dedicated in maintaining the resource pages for the long term. To help the databases check whether the URLs inserted in the articles are live, a table of all the database links is maintained for each article, after all the manual QC steps are completed. Database curators periodically check the URLs to make sure the links are live.
Unlike C. elegans articles, SGD articles require a stable and unique SGDID for each gene for correct linking. Since a few primary yeast gene symbols have changed or switched with another gene, manual quality control is needed to identify the correct SGDID for these ambiguous gene symbols, as well as ambiguous reagents. However, since the number of ambiguous names is very low, the manual effort is minimal. In the most recent twenty papers we processed, we found an average of one ambiguous entity in every two papers.
We have set up a pipeline for linking D. melanogaster articles to FlyBase. As noted earlier, because of the non-standard FlyBase nomenclature, only entities that are italicized are linked to FlyBase. This policy eliminates most of the false positives that occur from gene names that are also common English words. (This policy introduces false negatives when a gene name is not italicized, but the recall reduction was well worth the precision enhancement.) Nevertheless we noticed that this policy might still give rise to a few false positives for very short gene names (like N, P, a) since some of them are used for mathematical symbols, which are also italicized. Currently these false positives are unlinked at the manual QC step.
Having progressed with linking articles to SGD and Flybase, the next step of the project is linking entities from all databases should they occur together in the same paper. We have already carried out this task with the linking of both WormBase and SGD entities in Maduzia et al., 2010. . For this article, the source XML was first run through the WormBase linking script. The output of this script was then fed as input to the SGD linking script. Since there were no nomenclature clashes between WormBase and SGD entities in this paper, it was easy to process this article, and a minimal amount of QC was necessary beyond the normal QC for each database's entities.
Over the past five years, we have seen a push by databases to streamline data extraction from journal articles through a variety of methods including the development of text-mining tools, the development of stand-alone user interfaces that can mine and hyperlink journal articles, and through working directly with journals to request authors to provide a minimum amount of information to the database [1, 12–16]. Authors are valuable participants in our pipeline even though our experience with author participation demonstrates they are not completely reliable in providing the data we request. Our experience supports the results of the FEBS Letters experiment and the BioCreative II.5 challenge , in which author performance was determined to be relatively low, and further, their participation did not save trained curators any significant time in the identification and extraction of relevant data. We also agree with the conclusion of the BioCreative II.5 assessment that author participation is useful when combined with database-generated annotations, both human and machine. Regardless, we think that it is still very important to involve the authors in this pipeline. Ultimately, we hope that the more frequently authors are asked to participate in database curation efforts the more such participation becomes a standard part of having their work published.
We have a narrow goal in asking for author participation in this pipeline, that is, for them to help us link objects that do not exist in the database lexicon repository, and thus our database. We have taken advantage of this author submission pipeline to feed into a literature triage pipeline whereby data-type curators who are not part of this markup pipeline are alerted when there are new objects present in the paper, which will need curating. This latter use of author submissions is not a primary focus of this project, but it does provide valuable communication from which the author and our database benefits. Any level of participation from authors is beneficial to us; we are fortunate that we have had reasonable author participation.
The proper balance between automation and manual efforts
A recent article by Atwood et al.  presented a nice overview of the different hyperlinking tools currently available. While fully automated hyperlinking tools can provide instantaneous links, be portable enough to use on any online html page and can form links to any source, they are at a disadvantage when it comes to ensuring accuracy. By using a manual QC step we can selectively unlink ambiguous terms, ensuring that the reader is taken to the correct webpage. One suggested solution to resolve these ambiguities is to rely on user feedback and employ the reader to correct links, which is in use by Utopia Documents  and Reflect (relayed to us by one of anonymous reviewers). While this may prove an optimal solution for these fully automated tools, as we are starting from the point of the actual database that is being linked to, we might not benefit as much as these other projects. However, we are open to modifications of our pipeline that would increase our efficiency. As the most time consuming steps of this pipeline are the manual QC and XML editing we are actively developing tools to cut down on these steps. For example, we have created an interface that allows the curator to more easily view the marked up html as well as a list of the entities and links.
Benefits to the community
We established a manual QC step to resolve ambiguous or erroneous links that occur with automated linking. Automated tools cannot distinguish one entity from another entity with the same name, even if the entities are, for example, genes in entirely different species. Because of the well-established nomenclature in the C. elegans field, ambiguity is low for most of the entity classes. As we begin to link terms in classes that use a more familiar term such as the anatomy class, we have noted a rise in the number of links to resolve.
We use our QC step to enrich our database by identifying entities missing from our database. We also can take advantage of the QC step to link synonyms of terms to the appropriate community-approved name. These synonyms could represent jargon terms or author assigned names that did not follow community-based nomenclature rules when first adopted. For example, a researcher may have cloned a gene and assigned a name to it without first finding out if the gene name conflicts with a pre-existing class of genes soon to be published. In such cases, a link between the gene name used by the author can be made to the correct sequence page at the database, offsetting any confusion should the gene name get changed after the article is published.
By far the most important duty of this step is to resolve ambiguous links; however we have taken advantage of this step to feed important information back to the authors and journal as well as to enhance our own database. For example, we use the author first pass form to capture new entities that don't exist in our database. Combined with the manual QC step, we are able incorporate data in our database before the paper is published. In addition, our manual QC step has identified entities that had been discovered years ago but had not been entered into the database yet, which occurred for two papers.
Finally, our manual QC step has proved beneficial to the authors and journal as we have been able to catch typos and XML formatting errors that were missed by the authors and copy-editors.
The hardest hurdle in all of the hyperlinking efforts to date is resolving which species an ambiguous entity belongs to (see  for example). One automated method, Linneaus, has been developed to tackle the problem of identifying all gene names belonging to all species in an article without any prior knowledge of which species are discussed [19, 20]. However, our problem differs from others in that we have an advantage of knowing the different species discussed in an article a priori from the journal publisher and the authors. Hence the problem of species identification itself is not a major challenge we face. In addition, as noted, authors usually specify the species name near the entity should there be any ambiguity . For example, authors may use abbreviations (Sc for S. cerevisiae, Sp for Schizosaccharomyces pombe) before the entity name for disambiguation, which could be identified before linking is started. Finally, since we expand our pipeline one MOD at a time and work closely with MOD curators, identifying unique styles and conventions of writing scientific articles for each species could be captured and used for automatic disambiguation. While proximity of the species name to the entity does help in ambiguity resolution in most cases, such a heuristic approach may not work for all cases because of complexities in natural language texts. Ultimately, the manual QC step still remains the best way to identify and correct any errors arising out of automatic methods.
We are planning on linking articles from more model organisms and are looking for other databases and journals to actively participate in this project.
We thank members of WormBase, SGD, the GSA editorial board, Dartmouth Journal Services and FlyBase for helpful discussions and collaborations. We thank the anonymous reviewers for helpful critiques of the manuscript.
This work was funded in part by grants #R01- HG004090, #P41-HG002223, #P41 HG000739 and #P41-HG001315 from the National Human Genome Research Institute (NHGRI) at the United States National Institutes of Health. Work by TS was funded by GM63310 and GM085150. PWS is an investigator with the Howard Hughes Medical Institute.
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