• What is GFBio? expand_more

    The German Federation for Biological Data (GFBio) is a sustainable, service oriented, national data infrastructure facilitating data sharing for biological and environmental research. Find out more at www.gfbio.org.

  • Who are you and your partners? expand_more

    Please see the contact section.

  • What is your mission? expand_more

  • For whom are your services? expand_more

    Our service has two kinds of people in mind. On one hand, we are providing a single access point to various kinds of terminologies, ranging from simple controlled vocabularies to complex ontologies, for researchers of the biodiversity domain. This means, researchers are able to find, explore and share terminologies. On the other hand our service is for developers for whom the TS provides tools (API and widgets) to reuse terminologies for semantic enhancement of research platforms.

  • Are you working on the TS after GFBio finished? expand_more

  • Is there a fee to use your services? expand_more

  • What is the best way to cite you? expand_more

    Our suggested citation is as following:
    Karam, N.; Mueller-Birn, C.; Fichtmueller, D.; Gleisberg, M.; Bohlen, V; Tolksdorf, R. & Guentsch, A. (eds.) 2014 onwards. The Terminology Server of the German Federation for Biological Data (GFBio) - Server and service of semantic technologies in scientific environments. - hfalsettp://terminologies.gfbio.org/

About the Terminology Service

  • What are the TS and its objective? How does the TS work? expand_more

  • Why should I use the TS? expand_more

    If you are a researcher and searching for a single access to various terminologies in the biodiversity domain, you should use the TS. You can find the right one for your research and explore their terms. You even could share your own terminology with colleagues and other researchers. As a developer you can use the API and ready-made widgets based on the API we provided to reuse terminologies for semantic enhancement of your platform.

  • What does "semantic information" mean and how is it included in your work? expand_more

    The TS and its public API (Application Programming Interface) provide users with a machine-readable access to terms and their relations for a variety of biodiversity related data. The semantic information stems from the delivered metadata of any term, like the description, their synonyms or most notably the relationship to other terms (broader or narrower). With such information it is possible to classify and use the correct term.

  • What is a "terminology" in the GFBio context? expand_more

    The term "terminology" encompasses several meanings ranging from simple lists of terms to semantically rich ontologies. Unfortunately, there are currently no commonly accepted definitions of the different terminology types (in the biological domain) which leaves room for variation causing them to be used interchangeably depending on the context.
    GFBio distinguishes between five different types or formality levels of terminologies with differing levels of specification which are defined in the following section. Some of the terms may be used in a slightly different way in the scientific domain, a fact the user should be aware of when referring to terminologies outside the context of GFBio. Controlled Vocabulary The simplest type of terminology consisting in a finite list of terms without definitions or hierarchical ordering. Glossary A list of terms including an informal definition of their meaning in natural (human-readable) language. Since information expressed in natural language is typically not unambiguous, these specifications are not yet adequate for further processing by computer agents. Taxonomy/Classification A list of terms organized in a hierarchical structure, e.g., by is-afalse relationships, thus providing additional semantics in the relations between their terms which can be interpreted by computer agents. Thesaurus A controlled vocabulary connected via relations between the terms expressing hierarchies (e.g., “narrower/broader term”), associations (e.g., “related term”), or synonym relationships. Ontology An Ontology represents the highest level of formality a terminology can reach. It is a formal representation of a set of concepts and the relationships between them using semantically rich descriptions, allowing a n unambiguous interpretation of classes and term relationships according to logic-based rules.

  • What is a "term" in the TS context? expand_more

    A term is a single item of the appropriate terminology. As there are different types of terminologies (see above), terms are ranging from simple words without any definition or hierarchical relationship to other words to a rich concepts, owning attributes describing it profoundly and relationships linking it to other concepts.


  • What is the difference between internal and external terminologies? expand_more

    Internal terminologies are hosted locally at the Terminology Service in a Semantic Web repository. External terminologies are only registered at the Terminology Service and are remotely accessed via their own services. Seeing the term hierarchy or using the suggest functionality in the search works only for internal terminologies. Some metadata is not provided from external terminologies as well. The speed of the search in external terminologies relies on their API and is mostly slower than in internal ones.

  • Which terminologies are included in the Terminology Server? expand_more

    Among the terminologies currently included in the terminology server are:

    • Biological Collections Ontology (BCO)
    • Biodiversity Ecosystem Functioning Data (BEFDATA)
    • Chemical Entities of Biological Interest (ChEBI)
    • Environment Ontology (ENVO)
    • Geographic Region Ontology (GEOREGION)
    • Phenotypic Quality Ontology (PATO)

    The Terminology Server will be continuously enriched with new terminologies.

  • Which external terminologies are connected to the TS? expand_more

    The external terminologies currently connected to the TS are:

    • The Catalogue of Life (CoL)
    • The Integrated Taxonomic Information System (ITIS)
    • The World Register of Marine Species (WoRMS)
    • Fauna Europaea via PESI
    • The GeoNames geogr aphical database (Geonames)
    • The DWB REST Webservice for Taxon Lists (DTNtaxonlists)
    • The Prokaryotic Nomenclature Up-to-Date Taxon list (PNU)


  • What is the format of a downloaded terminology? expand_more

  • What happens when an external terminology is updated? Is there an update service? expand_more


  • Why should I contribute to the TS? expand_more

    You can provide your own terminologies to the Terminology Service and directly benefit from the offered services and tools. Your terminology will be available via our API and will be connected to the widgets for search and visualization.

  • How can I contribute to your service? What do I need to contribute to your service? expand_more

    At the moment you can contact us via email and send your terminology. Later, we will provide the possibility to upload files directly.

  • What happens after contributing to your service? expand_more

  • Is a contribution possible for people outside the biodiversity context? expand_more

    Yes, this is possible!