Free Text Gene Name Recognition

1)自2005年以来，我一直是BioCreative研讨会的共同组织者，并参加了BioCreative II（2007年），BioCreative III（2010年），BioCreative-2012研讨会（2012年）和BioCreative IV（2013年），我的小组正在参加BioCreative V（2015年），尚未发生。BioCreative研讨会的总体目标是促进文本挖掘和文本处理工具的开发，这些工具对生物科学的研究人员和数据库管理员社区有用。 2)我们目前正在努力开发更通用的方法，根据他们的摘要为PPI寻找高价值的文章。这项工作不仅涉及更强大的排名方法，还涉及向用户显示证据以供用户快速评估的方法。 3)我们还在研究一种命名实体识别方法，用于识别大量生物学上重要的实体类型。我们已经发现了某些通用模式，可以用来找到基因和其他实体类型，其可靠性高于通用CRF。这是一个正在进行的研究与更有用的一般模式的承诺。 4)我们已经开始了一个名为BioC的项目，该项目致力于创建一种由DTD定义的通用XML格式，并使用软件来读写这种格式。目前，这种方法已经在C++、Java、Python、Pearl、Ruby和GO中实现。其想法是使用这种通用货币来使对自然语言处理有用的软件模块更具互操作性。该项目还处于早期阶段，但我们已经有了使用上述语言进行读写的软件，以及使用这种方法的重要NLP处理模块，以及超过25个以该格式提供的黄金标准NLP注释数据集。该方法在BioCreative IV研讨会上得到了展示，并且该方法已经成为BioCreative V的BioC协作轨道的基础，该轨道将在短时间内举行。除了我们自己的团队之外，这条赛道还收到了八个团队的贡献，并建立了一个用户界面，向Biogrid策展人显示注释文章，以帮助他们工作。

1) I have been a co-organizer of the BioCreative Workshops since 2005 and have taken part in BioCreative II (2007), BioCreative III (2010), BioCreative-2012 Workshop (2012), and BioCreative IV (2013) and my group is taking part in BioCreative V (2015) which has not yet taken place. The overall goal of the BioCreative Workshops is to promote the development of text mining and text processing tools which are useful to the communities of researchers and database curators in the biological sciences. 2) We are currently working to develop more general methods of finding high value articles for PPI based on their abstracts. This effort involves not only more powerful ranking methods, but also ways to display evidence to the user for a users quick evaluation. 3) We are also investigating an approach to named entity recognition for a large number of biologically important entity types. We have found certain general patterns that can be used to find genes and other entity types with a higher reliability than can be done with a general CRF. This is ongoing research with a promise for more useful general patterns. 4) We have begun a project called BioC which is an effort to create a general XML format defined by a DTD and software to read and write this format. Currently this approach has been implemented in C++, Java, Python, Pearl, Ruby, and GO. The idea is to use this common currency to make software modules that are useful for natural language processing more interoperable. The project is in its early stages, but already we have software to read and write in the languages mentioned as well as significant NLP processing modules using this approach and over 25 gold standard NLP annotated data sets available in the format. The approach was featured in the BioCreative IV Workshop and the approach has formed the basis of the BioC Collaborative Track at BioCreative V which will take place in a short time. This track has received contributions from eight teams besides our own and has built a user interface which displays annotated articles to Biogrid curators to assist them in their work.