A huge problem in science today is the ability to quickly search the vast literature base and to accurately and efficiently find the data that you are interested in. Here at OpenHelix we focus on ways of effectively and efficiently get information out of public databases and resources, but at the other end of the process is the ability for scientific knowledge to be curated into those resources. We have featured biocurators and the phenomenal work that they do several times in the past, but it is work that never ends and can be very labor intensive. It often involves an initial triaging of a field’s literature, some level of automatic information gathering, and then careful manual effort on the part of scientist at the resource to gather and present the information through their site. I know from personal experience that the process of reading a paper, clarifying research details with an author, and then presenting that information to the author’s satisfaction can be a very long & labor intensive process, for both the curator AND the original author.

For years there has been discussion of ‘expert curation’ in which experts in the field author review or summary pages in a resource, or community curation jamborees, etc. And there have been fruits from many of these efforts, but in general participation is low. But who is more of an expert on the research being published other than the author himself? If authors could/would mark up their own papers during the publication process, not only could they be assured that it would be accurate but they would help make their research universally searchable without the lag required for searchability through a specific resource. Thus far document mark-up is has not been an easy process and has largely been deemed ‘not worth the effort’ for the level of attribution/recognition affiliated with it.

The BioMed Central article does a nice job of outlining and discussing many of these issues. It cites many other efforts and resources, explains their motivation and the implementation of their software. A nice feature of the tool is that there are interoperability features, and a real commitment to conforming with existing standards of practice. The article also presents an appendix of resource addresses of other groups involved in semantic searching and literature publication. I especially like this quote from the paper:

The Word add-in presented here will assist authors in this effort using community standards and by making it possible for the author of the document, the absolute expert on the content, to do so during the authoring process and to provide this information in the original source document.

You can also find brief tutorials on using the tool at SciVee: Word Add-in for Ontology Recognition Tutorial (1 of 4): Install Process

As a note, literature mark-up and enabling are currently an active area – Mary found another literature handling resource and paper as well: Check out the tip, the articles & the tools. Tell me what you find/think. Thanks! (OH, and Happy St. Patty’s to ya!)

UCSDBioLit Reference:

Fink, J., Fernicola, P., Chandran, R., Parastatidis, S., Wade, A., Naim, O., Quinn, G., & Bourne, P. (2010). Word add-in for ontology recognition: semantic enrichment of scientific literature BMC Bioinformatics, 11 (1) DOI: 10.1186/1471-2105-11-103

It may not surprise you that we at OpenHelix are pretty heavy-duty users of curated information from databases. It might surprise you to know that some of us have been involved in actually curating them as well. In both public and commercial situations, we’ve been on the curation side. And lately we’ve been heavily on the end-user side.

So we’ve been huge supporters of curators for a long time. We know that they are the ones responsible for the most trustworthy data in the databases. We know the intelligence, the focus, the attention to detail, and the training it takes to do this well.

Biocurators rock. If you do biomedical research and use the data from the databases, you can thank a biocurator.

But maybe you don’t know that much about exactly what biocurators do if you are mostly an end user of the databases. I’d like you to meet some of them. The new International Society for Biocuration has been established to foster development and respect for biocuration as a career choice and career path.

They are also currently holding an election for their board.  Have a look at the slate of candidates, and read some of those statements.  Check out the varied backgrounds on these folks–you’ll be seriously impressed with their skills and dedication to good data.

And if you are a biocurator, and a member of the society, I would encourage you to have a special look at Jennifer Williams of OpenHelix.  Jennifer is an incredible member of our team, and we totally support her candidacy for the ISB board.  She would bring useful skills to the job from the project management perspective, I assure you.  She knows both sides of curation equally well: getting data in and getting data out.  She’s also very much a bridge-builder with a very gentle and effective way of bringing people together in the right place.

In the continuing effort to get scientists and researchers to annotate and curate data and to capture the huge amount of knowledge available, UCSC Genome Browser has added a wiki annotation track to the browser. It’s not the first effort of course, GeneWiki is an effort, with mixed results so far, to annotate gene function information as a community exercise using Wikipedia. Some journals are requiring wiki entries, and several databases have opened wikis for curation. Wikis could be a solution for capturing the exponentially increasing amount of data,

or they could be just another place for adding confusion… or both. I suspect out of the plethora the wikis coming available for annotation and curation of genomic data, something will stick and find that Goldilocks balance of a dedicated community, ease of use, usability, and other aspects that will be needed for this to work.

Perhaps UCSC Genome Browser has that balance. It will remain to be seen, but let’s get started. Today’s tip is introducing the new wiki track in the UCSC Genome Browser.

The first examples of this program in action are already online. The journal is hosting an open access paper that describes a family of RNA molecules found in nematode worms; a corresponding Wikipedia page is already in place. In good Wikipedia form, the phylogenetic analysis of these RNAs is dinged for not providing citations, while the article as a whole is flagged as having excess jargon. (The talk page hosts an interesting discussion of how much jargon can possibly be eliminated from a highly technical description like this.)

So far, everyone is happy with the results. A few scientists have started updating the scientific content of the RNA entries, while the usual Wikipedia denizens have helped out in terms of catching typos and improving the formatting. The people backing the project expect that it will be immune to some of the issues that plague other Wikipedia entries; Nature quotes one of the biologists as saying, “”We don’t think vandalism will ever be as much of a problem for a Wikipedia page on transfer RNAs as it is for a page on George Bush.”

And looking at that one entry, it does seem to. But I have a question, if researchers are soon required not only to submit and/or annotate in a database and to wikis and curate and annotate if they wish to publish, doesn’t this start to place an undue burden on researchers who already have grant writing, teaching, and more in addition to actual research? There does need to be a solution to the growing need for curation and annotation of data, it will be interesting to see if this is one solution that will hold.

Now, I would use the form, and I would submit, and I would try to do it to meet standards and with accuracy. But I have had lots of colleagues over the years who would have blown that off. So I hope there is compliance, but….we’ll see. Over and over in bioinformatics there have been efforts at “community annotation” and “community submission” which have had mixed outcomes–both in adoption and quality. There are certainly some advocates and early adopters. Everybody wants great data in the databases when they go and look for it. But for the authors/submitters–it can be a time sink and a nuisance–without any benefit such as a CV item that the tenure committee will consider.

I even had one colleague who had submitted a gene to GenBank years ago and accidentally had a typo in the gene name. He knew he could correct it–but he preferred not to, because he knew that if he used the typo as a search he would always get his submission and not have to look through all the other ones.

Professional curation staff are so important for focus, volume, and quality control. They are serious and have such a great understanding of why the correct symbols, Gene Ontology terms, experimental descriptions, etc are crucial to store in the databases. But some scientists complain about the funding that goes to database projects because they compete for scarcer and scarcer resources with the bench researchers.

I wish this project great success. I would encourage people to take this seriously if you want good quality information in the databases. Community efforts are a great idea. But professional staff at these resources are still crucial for obtaining the quality we need in the databases. And for some efforts there really needs to be a committed group with training, standards, institutional memory and teamwork. I hope people support and appreciate curators as well.

Perhaps we’ll get a report on the TAIR/PlantPhysiol project at the next Biocurators meeting–we’ll be there, we’ll be looking forward to hearing about it!

Editorial: Plant Physiology 146:1022-1023 (2008)