Biocuration resources

Biocuration Resource Table - main table

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


Table 16 Biocuration Resource Table - metadatabase source

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INDRA

PCnet

FLUTE

OmniPath

3DComplex

X

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