3rd International BioCurator Meeting, April 16th - 19th, 2009, Berlin, Germany

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BioCurator Meeting Notes - Berlin, 2009 - Kimberly Van Auken

221 participants from 21 different countries

Community Annotation

work flow is an increasingly important concept in biocuration, not only for curators but for users who need to have a better understanding of how we do our work and what curation best practices are

collaborations with journals and authors to get semantic mark-ups of at least abstracts will be key, but so far there aren't a lot of success stories

have journals work with annotators/curators on papers prior to acceptance to make sure, for example, that issues of species designation, nomenclature, experimental details are resolved prior to publication

for existing author pipelines, e.g. TAIR, authors have needed to be pushed by journal editors to submit any data

with the exception of the maize database, it doesn't yet seem that author participation is widespread or saving much curation time when they do participate

some groups, e.g. IntAct, have emailed authors to ask if their data is represented correctly in the database the response rate was 10% but it still caught and corrected some errors

there needs to be a better reward system for authors to participate one possible reward being fast-tracking marked-up papers for publication and curation another being formal attribution by databases and inclusion of this work in people's CVs also, publicizing how many times a given paper is accessed through a link originating from a database

possible feedback to ask from authors: how much time did it take you to fill out this form? what difficulties did you have? were any data types unclear?

Text Mining

lots of interest in this session, but few examples of text mining incorporated into curation pipelines

having good dictionaries is key, many applications have tried to perform text mining using existing OBO ontologies but they haven't worked well yet

will there be standards for text mark-up and will different groups share their mark-ups

SwissProt tried machine learning methods and were 'very disappointed' in the outcome

detecting novel entities and information will be important for continued efficiency improvements

visualization of text mining returns (entities, sentences) in the actual PDF document was used by a number of groups and was nice for visualization and later curation

Curation Practices

there was a very heated debate in the functional genomics curation session about the role of curators in interpreting data

Mike Cusick, from Marc Vidal's group, took interaction database curators to task for not weeding out high throughput data, for example, or exercising more judgement in what they put into their databases (see their Nature Methods paper for specifics)

there seems to be two camps on this issue, i.e. to what extent should curators cull data before putting annotations into the database

it seems that most people (at least the curators) feel that their job is to present all published data in the database and inform users about how best to use it

others, however, including Mike Cusick and Amos Bairoch from SwissProt, feel that curators should use their biological expertise to be more selective about what they put in the database

no resolution, but it does raise the question of what do users really want from a database and how can we best educate people on how to use these resources

BioCurator Society

the society is now open for membership

Next Meeting

Fall, 2010, Japan Hosted by Takashi Gojobori, DDBJ