1. Catalog
  2. Namespaces

Namespaces

BEL borrows some ideas from the semantic web that resources at a given location should be persistent. However, the BEL namespace file format contains a flag to signify namespaces that might change over time that is only very narrowly appropriate for custom terminologies as they are under development. These namespaces are not cached and are not listed.

Public namespaces are distributed by Fraunhofer SCAI on the Artifactory server.

Keyword Name Version
21 Anatomy Uberon 20170511
1 bel BEL Default Namespace 2.1.1
81 BRCO Brain Region Ontology Terms 1.0.0
24 Cell Cell Ontology (CL) 20170511
22 CellLine Experimental Factor Ontology (EFO) 20170511
23 CellStructure MeSH 20170511
31 chebi ChEBI 20180828
75 chebi ChEBI 20180816
83 chebi ChEBI 20190224
3 chebi ChEBI 20180906
104 chebi ChEBI 20190224
48 CHEBI Chemical Entities of Biological Interest 02-01-2018
73 CL None None
25 Confidence Confidence 20170430
13 CTO Clinical Trial Ontology Terms 1.0.0
19 DBSNP None None
26 Disease Disease Ontology (DO) 20170511
46 DNSNP None None
14 DO Disease Ontology Names 20170725
88 doid doid releases/2019-03-01/doid.obo
4 drugbank DrugBank 20180906
89 drugbank DrugBank 20190224
90 ec-code Enzyme Nomenclature 20190224
5 ec-code Enzyme Nomenclature 20180906
68 ECCODE None None
67 FAMPLEX FamPlex 20180612
91 fb FlyBase 20181022
47 FPLX FamPlex 20190217
12 FPLX FamPlex 20180917
80 Gender Gender 20170430
62 GFAM HGNC Gene Families 20170710
49 go Gene Ontology 20181221
33 go Gene Ontology 20180828
107 go Gene Ontology 20190224
84 go Gene Ontology 20190224
61 go Gene Ontology 20180828
8 go Gene Ontology 20180921
76 go Gene Ontology 20180816
71 go Gene Ontology 20190207
74 HBP HBP 20180816
113 HBP Human Brain Pharmacome Terminology 20190416
11 HBP Human Brain Pharmacome Terminology 20181029
112 HBP Human Brain Pharmacome Terminology 20190310
105 HBP Human Brain Pharmacome Terminology 20190416
103 HBP Human Brain Pharmacome Terminology 20190222
102 HBP Human Brain Pharmacome Terminology 20190309
101 HBP Human Brain Pharmacome Terminology 20190208
100 HBP Human Brain Pharmacome Terminology 20190222
34 HBP Human Brain Pharmacome Terminology 20190206
43 HBP Human Brain Pharmacome Terminology 20181023
87 HBP Human Brain Pharmacome Terminology 20190310
51 HBP Human Brain Pharmacome Terminology 20181221
54 HBP Human Brain Pharmacome Terminology 20181221
55 HBP Human Brain Pharmacome Terminology 20181029
56 HBP Human Brain Pharmacome Terminology 20181128
82 HBP Human Brain Pharmacome Terminology 20190307
58 HBP Human Brain Pharmacome Terminology 20190126
59 HBP Human Brain Pharmacome Terminology 20190207
64 HBP Human Brain Pharmacome Terminology 20181212
65 HBP Human Brain Pharmacome Terminology 20181023
66 HBP None None
77 HBP Human Brain Pharmacome Terminology 20181119
9 hgnc HGNC 20180906
32 hgnc HGNC 20180828
106 hgnc HGNC 20190224
85 hgnc HGNC 20190224
50 HGNC HGNC Human Gene Names 20180215
63 hgnc.genefamily HGNC gene family 20181221
7 hgnc.genefamily gfam 20180906
114 hgnc.genefamily HGNC gene family 20190224
35 hgnc.genefamily gfam 20181015
92 hgnc.genefamily HGNC gene family 20190224
115 HM None None
93 hp hp releases/2019-02-12
15 HP human phenotype ontology 2017-10-05
94 interpro InterPro 20190224
36 interpro InterPro 20181021
18 INTERPRO InterPro Protein Families 20170731
57 mesh MeSH 20181007
45 mesh MeSH 20180906
2 mesh MeSH 20180828
60 mesh MeSH 20180828
44 mesh MeSH 20181007
108 MeSH mesh 20181007
86 MeSH mesh 20181007
37 MeSH mesh 20181007
69 MeSH mesh 20181007
27 MeSHAnatomy MeSH 20170511
70 MESHC MeSH Chemicals (Names) 20170725
28 MeSHDisease MeSH 20170511
109 mgi Mouse Genome Database 20190425
95 mgi Mouse Genome Database 20190224
38 mgi Mouse Genome Database 20181021
16 MGI MGI Approved Gene Symbols 20170725
96 mirbase miRBase 20180906
110 mirbase miRBase 20180906
10 mirbase miRBase 20180906
97 ncbigene NCBI Gene 20190224
6 ncbigene NCBI Gene 20180906
111 ncbigene NCBI Gene 20190224
72 NCBIGENE None None
98 pfam Pfam 20190224
39 pfam Pfam 20181024
42 PUBCHEM None None
99 rgd Rat Genome Database 20190224
40 rgd Rat Genome Database 20181021
17 RGD RGD Approved Gene Symbols 20170725
78 SCOMP Selventa Named Complexes 20170725
79 SFAM Named Protein Families 20170725
53 Species NCBI Taxonomy Ids 20170430
29 Subgraph NeuroMMSigDB 1.0.3
20 TAXONOMY None None
30 TextLocation Text Location 1.0.1
41 UNIPROT None None
52 UNIPROT None None

About

BEL Commons is developed and maintained in an academic capacity by Charles Tapley Hoyt and Daniel Domingo-Fernández at the Fraunhofer SCAI Department of Bioinformatics with support from the IMI project, AETIONOMY. It is built on top of PyBEL, an open source project. Please feel free to contact us here to give us feedback or report any issues. Also, see our Publishing Notes and Data Protection information.

If you find BEL Commons useful in your work, please consider citing: Hoyt, C. T., Domingo-Fernández, D., & Hofmann-Apitius, M. (2018). BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language. Database, 2018(3), 1–11.