1. Catalog
  2. Networks
  3. Perilous journey: a tour of the ubiquitin–proteasome system v1.0.0
  4. Compilation

Compilation Summary of Perilous journey: a tour of the ubiquitin–proteasome system 1.0.0

Table of Contents

  1. Namespaces
  2. Annotations
  3. Unused Namespaces
  4. Unused Annotations

Namespaces

This section lists all of the namespaces that are defined in the original BEL script.

CHEBI
https://raw.githubusercontent.com/pharmacome/terminology/b46b65c3da259b6e86026514dfececab7c22a11b/external/chebi-names.belns
CTO
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/clinical-trial-ontology/clinical-trial-ontology-1.0.0.belns
DO
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/disease-ontology/disease-ontology-20170725.belns
DRUGBANK
https://raw.githubusercontent.com/pharmacome/terminology/b46b65c3da259b6e86026514dfececab7c22a11b/external/drugbank-names.belns
ECCODE
https://raw.githubusercontent.com/pharmacome/terminology/b46b65c3da259b6e86026514dfececab7c22a11b/external/ec-code.belns
FPLX
https://raw.githubusercontent.com/sorgerlab/famplex/e8ae9926ff95266032cb74f77973c84939bffbeb/export/famplex.belns
GO
https://raw.githubusercontent.com/pharmacome/terminology/b46b65c3da259b6e86026514dfececab7c22a11b/external/go-names.belns
HBP
https://raw.githubusercontent.com/pharmacome/terminology/77c0796c3ca82a80cb0eaf1c8380d6ccd7f323af/export/hbp-names.belns
HGNC
https://raw.githubusercontent.com/pharmacome/terminology/b46b65c3da259b6e86026514dfececab7c22a11b/external/hgnc-names.belns
HGNCGENEFAMILY
https://raw.githubusercontent.com/pharmacome/terminology/3074b85b858455d8eeb76cfcdef685ced19bbe11/external/hgnc.genefamily-names.belns
HP
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/hp/hp-20171108.belns
INTERPRO
https://raw.githubusercontent.com/pharmacome/terminology/f2f993e599694ab5ce989cc39d789a499f75db99/external/interpro-names.belns
MESH
https://raw.githubusercontent.com/pharmacome/terminology/01c9daa61012b37dd0a1bc962521ba51a15b38f1/external/mesh-names.belns
MGI
https://raw.githubusercontent.com/pharmacome/terminology/f2f993e599694ab5ce989cc39d789a499f75db99/external/mgi-names.belns
MIRBASE
https://raw.githubusercontent.com/pharmacome/terminology/b46b65c3da259b6e86026514dfececab7c22a11b/external/mirbase-names.belns
NCBIGENE
https://raw.githubusercontent.com/pharmacome/terminology/b46b65c3da259b6e86026514dfececab7c22a11b/external/entrez.belns
PFAM
https://raw.githubusercontent.com/pharmacome/terminology/8ccfed235e418e4c8aa576f9a5ef0f838e794c7f/external/pfam-names.belns
RGD
https://raw.githubusercontent.com/pharmacome/terminology/f2f993e599694ab5ce989cc39d789a499f75db99/external/rgd-names.belns

Unused Namespaces 16

The source BEL script contained references to the following namespaces, but they were never used. It is suggested to delete their definitions from the BEL script to improve readability and parsing speed.

  • CTO
  • DBSNP
  • DO
  • DRUGBANK
  • ECCODE
  • FPLX
  • HGNCGENEFAMILY
  • HP
  • MGI
  • MIRBASE
  • NCBIGENE
  • PFAM
  • PUBCHEM
  • RGD
  • TAXONOMY
  • UNIPROT

Annotations

This section lists all of the annotations that are defined in the original BEL script.

Keyword URL Stratify
Anatomy https://arty.scai.fraunhofer.de/artifactory/bel/annotation/anatomy/anatomy-20170511.belanno View Stratified Summary
Cell https://arty.scai.fraunhofer.de/artifactory/bel/annotation/cell/cell-20170511.belanno View Stratified Summary
CellLine https://arty.scai.fraunhofer.de/artifactory/bel/annotation/cell-line/cell-line-20170511.belanno View Stratified Summary
CellStructure https://arty.scai.fraunhofer.de/artifactory/bel/annotation/cell-structure/cell-structure-20170511.belanno View Stratified Summary
Confidence https://arty.scai.fraunhofer.de/artifactory/bel/annotation/confidence/confidence-1.0.0.belanno View Stratified Summary
Disease https://arty.scai.fraunhofer.de/artifactory/bel/annotation/disease/disease-20170511.belanno View Stratified Summary
MeSHAnatomy https://arty.scai.fraunhofer.de/artifactory/bel/annotation/mesh-anatomy/mesh-anatomy-20170511.belanno View Stratified Summary
MeSHDisease https://arty.scai.fraunhofer.de/artifactory/bel/annotation/mesh-diseases/mesh-diseases-20170511.belanno View Stratified Summary
Subgraph https://arty.scai.fraunhofer.de/artifactory/bel/annotation/neurommsig/neurommsig-1.0.3.belanno View Stratified Summary
TextLocation https://arty.scai.fraunhofer.de/artifactory/bel/annotation/text-location/text-location-1.0.1.belanno View Stratified Summary

Unused Annotations 11

The source BEL script contained references to the following annotations, but they were never used. It is suggested to delete their definitions from the BEL script to improve readability and parsing speed.

Note: this may be due to errors occurring in all statements with these annotations.

  • Anatomy
  • Cell
  • CellLine
  • CellStructure
  • Confidence
  • Disease
  • MeSHAnatomy
  • MeSHDisease
  • Species
  • Subgraph
  • TextLocation

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.