MOTIVATION: Automated annotation of neuroanatomical connectivity statements from the neuroscience literature would enable accessible and large-scale connectivity resources. Unfortunately, the connectivity findings are not formally encoded and occur as natural language text. This hinders aggregation, indexing, searching and integration of the reports. We annotated a set of 1377 abstracts for connectivity relations to facilitate automated extraction of connectivity relationships from neuroscience literature. We tested several baseline measures based on co-occurrence and lexical rules. We compare results from seven machine learning methods adapted from the protein interaction extraction domain that employ part-of-speech, dependency and syntax features. RESULTS: Co-occurrence based methods provided high recall with weak precision. The shallow linguistic kernel recalled 70.1% of the sentence-level connectivity statements at 50.3% precision. Owing to its speed and simplicity, we applied the shallow linguistic kernel to a large set of new abstracts. To evaluate the results, we compared 2688 extracted connections with the Brain Architecture Management System (an existing database of rat connectivity). The extracted connections were connected in the Brain Architecture Management System at a rate of 63.5%, compared with 51.1% for co-occurring brain region pairs. We found that precision increases with the recency and frequency of the extracted relationships. AVAILABILITY AND IMPLEMENTATION: The source code, evaluations, documentation and other supplementary materials are available at http://www.chibi.ubc.ca/WhiteText. CONTACT: [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Online.

MOTIVATION: Many microarray datasets are available online with formalized standards describing the probe sequences and expression values. Unfortunately, the description, conditions and parameters of the experiments are less commonly formalized and often occur as natural language text. This hinders searching, high-throughput analysis, organization and integration of the datasets. RESULTS: We use the lexical resources and software tools from the Unified Medical Language System (UMLS) to extract concepts from text. We then link the UMLS concepts to classes in open biomedical ontologies. The result is accessible and clear semantic annotations of gene expression experiments. We applied the method to 595 expression experiments from Gemma, a resource for re-use and meta-analysis of gene expression profiling data. We evaluated and corrected all stages of the annotation process. The majority of missed annotations were due to a lack of cross-references. The most error-prone stage was the extraction of concepts from phrases. Final review of the annotations in context of the experiments revealed 89% precision. A naive system, lacking the phrase to concept corrections is 68% precise. We have integrated this annotation pipeline into Gemma. AVAILABILITY: The source code, documentation and Supplementary Materials are available at http://www.chibi.ubc.ca/GEOMMTX. The results of the manual evaluations are provided as Supplementary Material. Both manual and predicted annotations can be viewed and searched via the Gemma website at http://www.chibi.ubc.ca/Gemma. The complete set of predicted annotations is available as a machine readable resource description framework graph.