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
| blank | 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 |