Using reasoning to guide annotation with gene ontology terms in GOAT
ACM SIGMOD Record
Obol: integrating language and meaning in bio-ontologies: Conference Papers
Comparative and Functional Genomics
Granularity, scale and collectivity: when size does and does not matter
Journal of Biomedical Informatics - Special issue: Biomedical ontologies
NCI Thesaurus: A semantic model integrating cancer-related clinical and molecular information
Journal of Biomedical Informatics
Journal of Biomedical Informatics
The GENIA corpus: an annotated research abstract corpus in molecular biology domain
HLT '02 Proceedings of the second international conference on Human Language Technology Research
From GENIA to BIOTOPTowards a Top-Level Ontology for Biology
Proceedings of the 2006 conference on Formal Ontology in Information Systems: Proceedings of the Fourth International Conference (FOIS 2006)
Molecular interactions: On the ambiguity of ordinary statements in biomedical literature
Applied Ontology - Biomedical Ontology in Action
Desiderata for ontologies to be used in semantic annotation of biomedical documents
Journal of Biomedical Informatics
Building frame-based corpus on the basis of ontological domain knowledge
BioNLP '11 Proceedings of BioNLP 2011 Workshop
The use of foundational ontologies in ontology development: an empirical assessment
ESWC'11 Proceedings of the 8th extended semantic web conference on The semantic web: research and applications - Volume Part I
NLDB'11 Proceedings of the 16th international conference on Natural language processing and information systems
MedMatch - towards domain specific semantic matching
ICCS'11 Proceedings of the 19th international conference on Conceptual structures for discovering knowledge
Transforming semi-structured life science diagrams into meaningful domain ontologies with DiDOn
Journal of Biomedical Informatics
BioOntoVerb: A top level ontology based framework to populate biomedical ontologies from texts
Knowledge-Based Systems
Detecting and revising flaws in OWL object property expressions
EKAW'12 Proceedings of the 18th international conference on Knowledge Engineering and Knowledge Management
Evaluation of the OQuaRE framework for ontology quality
Expert Systems with Applications: An International Journal
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In the life sciences, there is an ample need for semantic interoperability of data. Thus shared vocabularies are needed for consistently expressing metadata in terms of semantic annotations as well as for querying bibliographic information systems. In the past years, lots of highly specialized, yet also fragmented terminologies have evolved. However, they lack principled forms of conceptual interlinkage. In order to provide an ontological basis for a seamless integration of such isolated parts of biological knowledge, we here introduce BioTop, an upper domain ontology for molecular biology. We describe its structure and contents, as well as its current interfaces to a selected set of OBO ontologies, which contain more detailed terminological knowledge about specific areas of molecular biology, e.g., cell types, molecular functions, biological processes and chemical compounds.