1. Catalog
  2. Networks
  3. Tau Modifications v1.9.5
  4. Compilation

Compilation Summary of Tau Modifications 1.9.5

Table of Contents

  1. Namespaces
  2. Annotations
  3. Unused Namespaces
  4. Unused Annotations
  5. Locally Defined Annotations
  6. Unused Locally Defined Annotations

Namespaces

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

BRCO
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/brain-region-ontology/brain-region-ontology-1.0.0.belns
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/90e1cb9e5e882703380c9db8d4915ac6f3cba137/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
SCOMP
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/selventa-named-complexes/selventa-named-complexes-20170725.belns
SFAM
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/selventa-protein-families/selventa-protein-families-20170725.belns

Unused Namespaces 12

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
  • DO
  • DRUGBANK
  • HGNCGENEFAMILY
  • HP
  • NCBIGENE
  • PFAM
  • PUBCHEM
  • SCOMP
  • SFAM
  • 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
Gender https://arty.scai.fraunhofer.de/artifactory/bel/annotation/gender/gender-1.0.0.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 5

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.

  • CellStructure
  • ExpGroup
  • MeSHAnatomy
  • Subgraph
  • TextLocation

Locally Defined Annotations 23

The source BEL script contained annotations defined as a list. Click each link to export the list definition as a BELANNO file that can hosted externally to promote re-usability and interoperability. After, you can replace the list definition in the source BEL with a SET ANNOTATION X AS URL "Y" definition.

Unused Locally Defined Annotations 8

The source BEL script contained the following list annotations, but no references to the following values. It is suggested to prune these values from the list definitions.

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

Annotation Values
Braak_Stage
  • Stage V
  • Stage IV
Cell_Line
  • HCN2A
  • COS7
  • CG-4
ExpGroup
  • healthy controls
HBP_Disease
  • Lewy Body Disease, Diffuse
  • Frontotemporal Lobar Degeneration
Km_ATP
  • 10 μM
Method
  • Pull-down Assay
  • Chromatography, Gel filtration
  • Laser Capture Microdissection
  • Protease-coupled Assay
  • Microtubule Co-Sedimentation Assay
  • RP HPLC
  • Microtubule polymerization Assay
  • RNA Interference, shRNA
  • Scanning electron microscopy (SEM)
  • Chromatography
  • F-actin depolymerization assay
  • Pull-down Assay, GST
  • In-vivo two photon calcium imaging
  • Microtubule Sedimentation Assay
  • Immunoaffinity Chromatography
  • LDH Assay
  • Tandem Affinity Purification, TAP
  • Chromatography, Affinity
  • Transmission electron microscopy (TEM)
  • Phosphorylation Assay
  • Pull-down assay, His-tagged
  • Electron Microscopy, Immunological
  • Microtubule-binding Assay
  • Pull-down assay, GST
  • Immunofluorescence Imaging
  • Comet Assay
  • Pull-down Assay, GFP
  • Enhanced Chemioluminescence visualization (ECL)
  • In vitro actin-bundling assay
  • Co-Immunoprecipitation
  • Ubiquitination Assay
  • Non-denaturing Fast Halo Assay
  • Degradation Assay, 20S Proteasomal
  • Chromatography, FPLC
  • Dephosphorylation Assay
  • Confocal Microscopy, Laser Scanning
  • Yeast Two-Hybrid Assay
  • Chromatography, Ni-NTA-Sepharose
  • Immunocytochemistry
  • Dephosphorylation Assay, Colorimetric
  • Surface Plasmon Resonance
  • Terminal Continuation RNA Amplification
  • Microarray
  • Chymotrypsin Assay
  • Deglycosylation Assay
Research_Model
  • K3 model with hyperphoshorylated tau resembling FTD
Vmax
  • 656 nM/min/mg
  • 59 μM

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.