Biocuration resources
Name |
GO (Gene Ontology) |
miRBase |
UniProt |
ChEBI |
BioGRID |
HPRD |
KEGG |
MINT |
PathwayCommons |
Reactome |
SIGNOR |
STITCH |
STRING |
WikiPathways |
FLUTE |
INDRA |
IntAct |
OmniPath |
PCnet |
BioModels |
CellCollective |
Path2Models |
MINERVA |
BioKC |
nDex |
REACH |
RLIMS-P |
Sparser |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Type |
Entity database |
Entity database |
Entity database |
Entity database |
Interaction database |
Interaction database |
Interaction database |
Interaction database |
Interaction database |
Interaction database |
Interaction database |
Interaction database |
Interaction database |
Interaction database |
Metadatabase |
Metadatabase |
Metadatabase |
Metadatabase |
Metadatabase |
Model repository |
Model repository |
Model repository |
Model repository |
Model repository |
Model repository/metadatabase |
Reader |
Reader |
Reader |
Curation? (Manual/Automated) |
Maual and automated |
Manual (staff curators) |
Maual and automated |
Manual (staff curators) |
Manual and automated |
Manual (staff curators) |
Manual (staff curators and data providers) |
Manual (registered users) |
Manual (from data providers) |
Manual (staff curators) |
Manual (staff curators) |
Manual and automated |
Manual and automated |
Manual (registered users) |
Manual (staff curators) |
Manual and automated |
Manual (staff curators) |
Manual (staff curators) |
Manual (staff curators) |
Manual (registered users) |
Manual (registered users) |
Automated (from other databases) |
Manual (registered users) |
Manual (registered users) |
Manual (registered users) |
N/A |
N/A |
N/A |
Programmatic access? |
Yes (API) |
No |
Yes (API) |
Yes (Web service) |
Yes (API) |
No |
Yes (API) |
Yes (API) |
No |
Yes (API) |
Yes (API) |
Yes (API) |
Yes (API) |
No |
Yes (Python script) |
Yes (API) |
No |
Yes (API) |
No |
No |
No |
No |
Yes (API) |
Yes (API) |
Yes (API) |
Yes (API) |
No |
Yes (Lisp) |
Input format |
N/A |
N/A |
N/A |
N/A |
N/A |
N/A |
N/A |
N/A |
N/A |
N/A |
N/A |
N/A |
N/A |
GPML |
N/A |
N/A |
N/A |
N/A |
N/A |
SBML (preferred), CellML, matlab |
SBML, boolean expressions |
N/A |
SBML |
SBML |
CX |
NXML, text |
Keywords, PMIDs |
Text, XML |
Output format |
OWL, OBO, GAF, etc. |
FASTA, EMBL |
FASTA, TSV, XML, JSON, etc. |
Molfile, XML, SDF |
PSI-MITAB, XML, BioGRID TAB |
BioPAX, SBML, PSI-MI |
KGML, PNG |
MITAB |
PNG, SIF, JSON, SBGN, BioPAX |
SBML, BioPAX, SBGN,PNG |
SBML, TSV |
TSV, PNG, XML, MFA |
TSV, PNG, XML, MFA |
PNG, JSON, GPML, SVG |
BioRECIPE, SIF |
PySB, SBML, BEL, JSON |
PSI-MITAB |
SIF |
SIF |
SBML,XPP, VCML, SciLab, Octave, BioPAX, PNG, SVG |
SBML, GML, truth tables, boolean expressions |
SBML,XPP, VCML, SciLab, Octave, BioPAX, PNG, SVG |
CellDesigner SBML, SBML, SBGN, PNG |
TSV, CX |
JSON,TSV |
TSV |
None |
|
Number of models/pathways/interactions if database |
43,850 GO terms / 7,928,834 annotations /1,568,828 gene products |
38,589 miRNAs |
569,213 reviewed / 245,871,679 unreviewed proteins |
151,344 substances / 139,678 annotations |
>3 million interactions |
>40,000 PPI, 36 pathways |
70,423 references |
136,218 interactions |
5,772 pathways /2,424,055 interactions/ 22 databases |
13,827 interactions / 2536 pathways |
29,245 interactions |
1.6 billion interactions |
>20 billion interactions |
>1,100 pathways |
30 million+ interactions |
N/A |
5,565,271 interactions |
100+ networks/databases |
21 networks/databases |
2,914 models |
229 models |
~140,00 models |
9 networks |
No public networks |
>5,000 networks |
N/A |
N/A |
N/A |
Systems modeled? |
Multiple species |
Multiple species |
Multiple species |
Multiple species |
Multiple species |
Homo sapiens |
Multiple Species |
Multiple Species |
Multiple species |
Homo sapiens |
Homo sapiens, Mus musculus, Rattus norvegicus |
Multiple species |
Multiple species |
Multiple species |
Homo sapiens |
Multiple Species |
Multiple Species |
Multiple Species |
Homo sapiens |
Multiple species |
Multiple species |
Multiple Species |
Multiple species |
Multiple species |
Multiple species |
N/A |
N/A |
N/A |
Automated verification or validation? |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
Has model-checking function |
No |
No |
No |
No |
Yes (simulation) |
No |
Yes (model annotation requirements) |
Yes (model annotation requirements) |
No |
No |
No |
No |
Automated filtering? |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
Belief score |
No |
No |
No |
No |
No |
Models are sorted by genus |
No |
No |
No |
No |
No |
No |
Automated identification of extensions/contradictions |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
Automatically resolve contradictions? |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
Automated recommendations? |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
Yes |
Yes |
No |
No |
No |
No |
No |
No |
No |
No |
No |
No |
Yes |
No |
No |
No |
No |
ChEBI: Chemical Entities of Biological Interest
BioGRID: The Biological General Repository for Interaction Datasets
HPRD: Human Protein Reference Database
KEGG: Kyoto Encyclopedia of Genes and Genomes
MINT: Molecular Interaction Database
SIGNOR: Signaling Network Open Resource
STITCH: Search Tool for Interacting Chemicals
STRING: Search Tool for Retrieval of Interacting Genes/Proteins
FLUTE: FiLter for Understanding True Events
INDRA: Integrated Network and Dynamical Reasoning Assembler
PCnet: Parsimonius Composite Network
nDex: The Network Data Exchange
REACH: Reading and Assembling Contextual and Holistic Mechanisms from Text
RRLIMS-P: Rule-based Literature Mining System for Protein Phosphorylation
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INDRA |
PCnet |
FLUTE |
OmniPath |
---|---|---|---|---|
3DComplex |
X |
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ABS |
X |
|||
ACSN |
X |
X |
||
Adhesome |
X |
|||
AlzPathway |
X |
|||
ARACNe |
X |
|||
ARN |
X |
|||
Ataxia |
X |
|||
BIND |
X |
|||
BioCarta |
X |
|||
BioGRID |
X |
X |
X |
X |
BioPLEX |
X |
|||
CancerCellMap |
X |
|||
CancerDrugsDB |
X |
|||
CancerSEA |
X |
|||
CARFMAP |
X |
|||
CellCall |
X |
|||
CellCellInteractions |
X |
|||
CellChatDB |
X |
|||
Cellinker |
X |
|||
CellPhoneDB |
X |
|||
cellsignal.com |
X |
|||
CellTalkDB |
X |
|||
CellTypist |
X |
|||
CFinder |
X |
|||
Compleat |
X |
|||
ComplexPortal |
X |
|||
ComPPI |
X |
|||
connectomeDB2020 |
X |