Background: Lately, there has been a great interest in the application of information extraction methods to the biomedical domain, in particular, to the extraction of relationships of genes, proteins, and RNA from scientific publications. The development and evaluation of such methods requires annotated domain corpora. We present BioInfer (Bio Information Extraction Resource), a new public resource providing an annotated corpus of biomedical English. We describe an annotation scheme capturing named entities and their relationships along with a dependency analysis of sentence syntax. We further present ontologies defining the types of entities and relationships annotated in the corpus. Currently, the corpus contains 1100 sentences from abstracts of biomedical research articles annotated for relationships, named entities, as well as syntactic dependencies. Supporting software is provided with the corpus. The corpus is unique in the domain in combining these annotation types for a single set of sentences, and in the level of detail of the relationship annotation. We introduce a corpus targeted at protein, gene, and RNA relationships which serves as a resource for the development of information extraction systems and their components such as parsers and domain analyzers. The corpus will be maintained and further developed with a current version being available at Figure 1 Dependency annotation example. The link labels represent types of dependency, for example, S for subject-predicate and O for predicate-object dependency. Deletion of SIR4 enhanced MET15 silencing . M S J AN O BMC Bioinformatics 2007, 8:50 The sentence The inhibitory action of p27, a cyclin-dependent kinase inhibitor (CDKI), arises from its binding with the cyclin E/Cdk2 complex that results in G(1)-S arrest. Entities and types · p27 -individual protein · action of p27 -function property · cyclin-dependent kinase inhibitor -protein family or group · CDKI -protein family or group protein Ontology knowledge about entity types · individual protein ≺ protein ≺ amino acid ≺ organic ≺ compound ≺ substance ≺ physical entity ≺ entity · protein family or group ≺ protein ≺ amino acid ≺ organic ≺ compound ≺ substance ≺ physical entity ≺ entity · protein complex ≺ individual protein ≺ protein ≺ amino acid ≺ organic ≺ compound ≺ substance ≺ physical entity ≺ entity · function property ≺ property ≺ entity Relationships · EQUAL(cyclin-dependent kinase inhibitor, CDKI) · MEMBER(cyclin-dependent kinase inhibitor, p27) · ANAPHORA(its, p27) · CONTAIN(cyclin E/Cdk2 complex, cyclin E) · CONTAIN(cyclin E/Cdk2 complex, Cdk2) · CAUSE(BIND(its, cyclin E/Cdk2 complex), action of p27) Ontology knowledge about relationships · EQUAL ≺ equality ≺ is a ≺ relationship · MEMBER ≺ collection:member ≺ part of ≺ relationship · CONTAIN ≺ object:component ≺ part of ≺ relationship · CAUSE ≺ causal ≺ relationship · BIND ≺ assembly ≺ physical ≺ change ≺ causal ≺ relationship Text binding, i.e. text used to infer the relationships · CONTAIN : complex · CAUSE : arises from · BIND: binding with Syntactic annotation m its binding with the cyclin E/Cdk2 complex that results in G(1)-S arrest . J DP MV J D AN AN B R RS MV J AN The inhibitory action of p27 , a cyclin-dependent kinase inhibitor ( CDKI ) , arises from D A S M J MX D AN AN MX MV
The BioInfer corpus REF contains 1,100 sentences from abstracts of research articles where biomedical relations are annotated for negation.
BioInfer: a corpus for information extraction in the biomedical domain
BMC Bioinformatics
BMC Bioinformatics
Computer Science Medicine