OntoGene Bio Term Hub

The Bio Term Hub (BTH) can be used to download selected terminological resources in a simple text format, or it can be used to annotate user-provided text. In both cases, select the desired resources, then press the button Create resource at the bottom of the page.

The BTH has been developed by the OntoGene/BioMeXT group. For information, requests and suggestions please contact Fabio Rinaldi.

Resource Selection

select all

 Cell Ontology

(→ source)

2024-09-20

The Bio Term Hub provides access to biomedical terminology resources in a unified format. We envision its main use as a basis for text mining systems.

Select any of the external resources on the left to obtain a custom terminology list. The list is a tab-separated table with the following six fields: 

CUI, source, native ID, term, preferred name, entity type
Each term (name/synonym) is on a separate row. As a recent addition (January 2019), the corresponding UMLS identifier (CUI) is given in the first column, if defined. The contents of the fields source and entity type can be modified using replacement patterns (uncover the Renaming section below using the triangle button). Submit your request with the Create resource button at the bottom of the page. Afterwards you will be offered the opportunity to annotate a text with the selected resources.

Aggregating, filtering, reformatting, and optionally renaming all this information takes time. Creation time mainly depends on the size of each resource. Compiling a list of all terminologies except for EntrezGene takes approximately 90 seconds; however, EntrezGene is very large, and processing it requires 3 to 4 minutes.

The requested terminology list is compiled on the fly, based on local copies of the external terminology resources. Whenever one of the local copies becomes out-of-date with respect to its remote source, an Update button is shown next to the corresponding resource name. This button triggers downloading the latest version to our server. Please note that, due to data volume and bandwidth restrictions, updating may take several minutes for some of the resources.

 Cellosaurus

(→ source)

2024-05-14

 ChEBI

(→ source)

2023-10-12

 CTD chemicals

(→ source)

2020-02-23

 CTD diseases

(→ source)

2024-08-22

 EntrezGene

(→ source)

2024-08-22

 Gene Ontology

(→ source)

2024-08-22

 MeSH

(→ source)

2024-05-14

 Molecular Process Ontology

(→ source)

2023-02-20

 NCBI Taxonomy

(→ source)

2024-05-14

 Protein Ontology

(→ source)

2021-01-19

 RxNorm

(→ source)

2024-08-22

 Sequence Ontology

(→ source)

2020-09-13

 Swiss-Prot

(→ source)

2024-05-14

 Uberon

(→ source)

2024-05-14

 skip CTD entries that are MeSH duplicates
(has no effect unless both CTD and MeSH are selected)

 remove very short terms (1 or 2 characters) and plain numbers

 create universal, HTTP-based identifiers (URI)

Disclaimer: The Bio Term Hub is a derivative service providing access to publicly available terminology resources. Licenses and agreements might apply to individual resources; please refer to the original sources.

     download as Zip archive  create term-statistics plots

If you use the Bio Term Hub in academic work, please cite the following paper:

Ellendorff, Tilia Renate; van der Lek, Adrian; Furrer, Lenz; Rinaldi, Fabio: A Combined Resource of Biomedical Terminology and its Statistics. In: Poibeau, T., Faber, P. (eds.) Proceedings of the 11th International Conference on Terminology and Artificial Intelligence, Granada, Spain, pp. 39–49 (2015)