@synsci/cli-darwin-x64-baseline 1.1.76 → 1.1.78

package/bin/skills/uniprot-database/references/api_fields.md

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+# UniProt API Fields Reference
+
+Complete list of available fields for customizing UniProt API queries. Use these fields with the `fields` parameter to retrieve only the data you need.
+
+## Usage
+
+Add fields parameter to your query:
+```
+https://rest.uniprot.org/uniprotkb/search?query=insulin&fields=accession,gene_names,organism_name,length
+```
+
+Multiple fields are comma-separated. No spaces after commas.
+
+## Core Fields
+
+### Identification
+- `accession` - Primary accession number (e.g., P12345)
+- `id` - Entry name (e.g., INSR_HUMAN)
+- `uniprotkb_id` - Same as id
+- `entryType` - REVIEWED (Swiss-Prot) or UNREVIEWED (TrEMBL)
+
+### Protein Names
+- `protein_name` - Recommended and alternative protein names
+- `gene_names` - Gene name(s)
+- `gene_primary` - Primary gene name
+- `gene_synonym` - Gene synonyms
+- `gene_oln` - Ordered locus names
+- `gene_orf` - ORF names
+
+### Organism Information
+- `organism_name` - Organism scientific name
+- `organism_id` - NCBI taxonomy identifier
+- `lineage` - Taxonomic lineage
+- `virus_hosts` - Virus host organisms (for viral proteins)
+
+### Sequence Information
+- `sequence` - Amino acid sequence
+- `length` - Sequence length
+- `mass` - Molecular mass (Daltons)
+- `fragment` - Whether entry is a fragment
+- `checksum` - Sequence CRC64 checksum
+
+## Annotation Fields
+
+### Function and Biology
+- `cc_function` - Function description
+- `cc_catalytic_activity` - Catalytic activity
+- `cc_activity_regulation` - Activity regulation
+- `cc_pathway` - Metabolic pathway information
+- `cc_cofactor` - Cofactor information
+
+### Interaction and Localization
+- `cc_interaction` - Protein-protein interactions
+- `cc_subunit` - Subunit structure
+- `cc_subcellular_location` - Subcellular location
+- `cc_tissue_specificity` - Tissue specificity
+- `cc_developmental_stage` - Developmental stage expression
+
+### Disease and Phenotype
+- `cc_disease` - Disease associations
+- `cc_disruption_phenotype` - Disruption phenotype
+- `cc_allergen` - Allergen information
+- `cc_toxic_dose` - Toxic dose information
+
+### Post-translational Modifications
+- `cc_ptm` - Post-translational modifications
+- `cc_mass_spectrometry` - Mass spectrometry data
+
+### Other Comments
+- `cc_alternative_products` - Alternative products (isoforms)
+- `cc_polymorphism` - Polymorphism information
+- `cc_rna_editing` - RNA editing
+- `cc_caution` - Caution notes
+- `cc_miscellaneous` - Miscellaneous information
+- `cc_similarity` - Sequence similarities
+- `cc_sequence_caution` - Sequence caution
+- `cc_web_resource` - Web resources
+
+## Feature Fields (ft_)
+
+### Molecular Processing
+- `ft_signal` - Signal peptide
+- `ft_transit` - Transit peptide
+- `ft_init_met` - Initiator methionine
+- `ft_propep` - Propeptide
+- `ft_chain` - Chain (mature protein)
+- `ft_peptide` - Peptide
+
+### Regions and Sites
+- `ft_domain` - Domain
+- `ft_repeat` - Repeat
+- `ft_ca_bind` - Calcium binding
+- `ft_zn_fing` - Zinc finger
+- `ft_dna_bind` - DNA binding
+- `ft_np_bind` - Nucleotide binding
+- `ft_region` - Region of interest
+- `ft_coiled` - Coiled coil
+- `ft_motif` - Short sequence motif
+- `ft_compbias` - Compositional bias
+
+### Sites and Modifications
+- `ft_act_site` - Active site
+- `ft_metal` - Metal binding
+- `ft_binding` - Binding site
+- `ft_site` - Site
+- `ft_mod_res` - Modified residue
+- `ft_lipid` - Lipidation
+- `ft_carbohyd` - Glycosylation
+- `ft_disulfid` - Disulfide bond
+- `ft_crosslnk` - Cross-link
+
+### Structural Features
+- `ft_helix` - Helix
+- `ft_strand` - Beta strand
+- `ft_turn` - Turn
+- `ft_transmem` - Transmembrane region
+- `ft_intramem` - Intramembrane region
+- `ft_topo_dom` - Topological domain
+
+### Variation and Conflict
+- `ft_variant` - Natural variant
+- `ft_var_seq` - Alternative sequence
+- `ft_mutagen` - Mutagenesis
+- `ft_unsure` - Unsure residue
+- `ft_conflict` - Sequence conflict
+- `ft_non_cons` - Non-consecutive residues
+- `ft_non_ter` - Non-terminal residue
+- `ft_non_std` - Non-standard residue
+
+## Gene Ontology (GO)
+
+- `go` - All GO terms
+- `go_p` - Biological process
+- `go_c` - Cellular component
+- `go_f` - Molecular function
+- `go_id` - GO term identifiers
+
+## Cross-References (xref_)
+
+### Sequence Databases
+- `xref_embl` - EMBL/GenBank/DDBJ
+- `xref_refseq` - RefSeq
+- `xref_ccds` - CCDS
+- `xref_pir` - PIR
+
+### 3D Structure Databases
+- `xref_pdb` - Protein Data Bank
+- `xref_pcddb` - PCD database
+- `xref_alphafolddb` - AlphaFold database
+- `xref_smr` - SWISS-MODEL Repository
+
+### Protein Family/Domain Databases
+- `xref_interpro` - InterPro
+- `xref_pfam` - Pfam
+- `xref_prosite` - PROSITE
+- `xref_smart` - SMART
+
+### Genome Databases
+- `xref_ensembl` - Ensembl
+- `xref_ensemblgenomes` - Ensembl Genomes
+- `xref_geneid` - Entrez Gene
+- `xref_kegg` - KEGG
+
+### Organism-Specific Databases
+- `xref_mgi` - MGI (mouse)
+- `xref_rgd` - RGD (rat)
+- `xref_flybase` - FlyBase (fly)
+- `xref_wormbase` - WormBase (worm)
+- `xref_xenbase` - Xenbase (frog)
+- `xref_zfin` - ZFIN (zebrafish)
+
+### Pathway Databases
+- `xref_reactome` - Reactome
+- `xref_signor` - SIGNOR
+- `xref_signalink` - SignaLink
+
+### Disease Databases
+- `xref_disgenet` - DisGeNET
+- `xref_malacards` - MalaCards
+- `xref_omim` - OMIM
+- `xref_orphanet` - Orphanet
+
+### Drug Databases
+- `xref_chembl` - ChEMBL
+- `xref_drugbank` - DrugBank
+- `xref_guidetopharmacology` - Guide to Pharmacology
+
+### Expression Databases
+- `xref_bgee` - Bgee
+- `xref_expressionetatlas` - Expression Atlas
+- `xref_genevisible` - Genevisible
+
+## Metadata Fields
+
+### Dates
+- `date_created` - Entry creation date
+- `date_modified` - Last modification date
+- `date_sequence_modified` - Last sequence modification date
+
+### Evidence and Quality
+- `annotation_score` - Annotation score (1-5)
+- `protein_existence` - Protein existence level
+- `reviewed` - Whether entry is reviewed (Swiss-Prot)
+
+### Literature
+- `lit_pubmed_id` - PubMed identifiers
+- `lit_doi` - DOI identifiers
+
+### Proteomics
+- `proteome` - Proteome identifier
+- `tools` - Tools used for annotation
+
+## Retrieving Available Fields Programmatically
+
+Use the configuration endpoint to get all available fields:
+```bash
+curl https://rest.uniprot.org/configure/uniprotkb/result-fields
+```
+
+Or in Python:
+```python
+import requests
+response = requests.get("https://rest.uniprot.org/configure/uniprotkb/result-fields")
+fields = response.json()
+```
+
+## Common Field Combinations
+
+### Basic protein information
+```
+fields=accession,id,protein_name,gene_names,organism_name,length
+```
+
+### Sequence and structure
+```
+fields=accession,sequence,length,mass,xref_pdb,xref_alphafolddb
+```
+
+### Functional annotation
+```
+fields=accession,protein_name,cc_function,cc_catalytic_activity,cc_pathway,go
+```
+
+### Disease information
+```
+fields=accession,protein_name,gene_names,cc_disease,xref_omim,xref_malacards
+```
+
+### Expression patterns
+```
+fields=accession,gene_names,cc_tissue_specificity,cc_developmental_stage,xref_bgee
+```
+
+### Complete annotation
+```
+fields=accession,id,protein_name,gene_names,organism_name,sequence,length,cc_*,ft_*,go,xref_pdb
+```
+
+## Notes
+
+1. **Wildcards**: Some fields support wildcards (e.g., `cc_*` for all comment fields, `ft_*` for all features)
+
+2. **Performance**: Requesting fewer fields improves response time and reduces bandwidth
+
+3. **Format dependency**: Some fields may be formatted differently depending on output format (JSON vs TSV)
+
+4. **Null values**: Fields without data may be omitted from response (JSON) or empty (TSV)
+
+5. **Arrays vs strings**: In JSON format, many fields return arrays of objects rather than simple strings
+
+## Resources
+
+- Interactive field explorer: https://www.uniprot.org/api-documentation
+- API fields endpoint: https://rest.uniprot.org/configure/uniprotkb/result-fields
+- Return fields documentation: https://www.uniprot.org/help/return_fields

package/bin/skills/uniprot-database/references/id_mapping_databases.md

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+# UniProt ID Mapping Databases
+
+Complete list of databases supported by the UniProt ID Mapping service. Use these database names when calling the ID mapping API.
+
+## Retrieving Database List Programmatically
+
+```python
+import requests
+response = requests.get("https://rest.uniprot.org/configure/idmapping/fields")
+databases = response.json()
+```
+
+## UniProt Databases
+
+### UniProtKB
+- `UniProtKB_AC-ID` - UniProt accession and ID
+- `UniProtKB` - UniProt Knowledgebase
+- `UniProtKB-Swiss-Prot` - Reviewed (Swiss-Prot)
+- `UniProtKB-TrEMBL` - Unreviewed (TrEMBL)
+- `UniParc` - UniProt Archive
+- `UniRef50` - UniRef 50% identity clusters
+- `UniRef90` - UniRef 90% identity clusters
+- `UniRef100` - UniRef 100% identity clusters
+
+## Sequence Databases
+
+### Nucleotide Sequence
+- `EMBL` - EMBL/GenBank/DDBJ
+- `EMBL-CDS` - EMBL coding sequences
+- `RefSeq_Nucleotide` - RefSeq nucleotide sequences
+- `CCDS` - Consensus CDS
+
+### Protein Sequence
+- `RefSeq_Protein` - RefSeq protein sequences
+- `PIR` - Protein Information Resource
+
+## Gene Databases
+
+- `GeneID` - Entrez Gene
+- `Gene_Name` - Gene name
+- `Gene_Synonym` - Gene synonym
+- `Gene_OrderedLocusName` - Ordered locus name
+- `Gene_ORFName` - ORF name
+
+## Genome Databases
+
+### General
+- `Ensembl` - Ensembl
+- `EnsemblGenomes` - Ensembl Genomes
+- `EnsemblGenomes_PRO` - Ensembl Genomes protein
+- `EnsemblGenomes_TRS` - Ensembl Genomes transcript
+- `Ensembl_PRO` - Ensembl protein
+- `Ensembl_TRS` - Ensembl transcript
+
+### Organism-Specific
+- `KEGG` - KEGG Genes
+- `PATRIC` - PATRIC
+- `UCSC` - UCSC Genome Browser
+- `VectorBase` - VectorBase
+- `WBParaSite` - WormBase ParaSite
+
+## Structure Databases
+
+- `PDB` - Protein Data Bank
+- `AlphaFoldDB` - AlphaFold Database
+- `BMRB` - Biological Magnetic Resonance Data Bank
+- `PDBsum` - PDB summary
+- `SASBDB` - Small Angle Scattering Biological Data Bank
+- `SMR` - SWISS-MODEL Repository
+
+## Protein Family and Domain Databases
+
+- `InterPro` - InterPro
+- `Pfam` - Pfam protein families
+- `PROSITE` - PROSITE
+- `SMART` - SMART domains
+- `CDD` - Conserved Domain Database
+- `HAMAP` - HAMAP
+- `PANTHER` - PANTHER
+- `PRINTS` - PRINTS
+- `ProDom` - ProDom
+- `SFLD` - Structure-Function Linkage Database
+- `SUPFAM` - SUPERFAMILY
+- `TIGRFAMs` - TIGRFAMs
+
+## Organism-Specific Databases
+
+### Model Organisms
+- `MGI` - Mouse Genome Informatics
+- `RGD` - Rat Genome Database
+- `FlyBase` - FlyBase (Drosophila)
+- `WormBase` - WormBase (C. elegans)
+- `Xenbase` - Xenbase (Xenopus)
+- `ZFIN` - Zebrafish Information Network
+- `dictyBase` - dictyBase (Dictyostelium)
+- `EcoGene` - EcoGene (E. coli)
+- `SGD` - Saccharomyces Genome Database (yeast)
+- `PomBase` - PomBase (S. pombe)
+- `TAIR` - The Arabidopsis Information Resource
+
+### Human-Specific
+- `HGNC` - HUGO Gene Nomenclature Committee
+- `CCDS` - Consensus Coding Sequence Database
+
+## Pathway Databases
+
+- `Reactome` - Reactome
+- `BioCyc` - BioCyc
+- `PlantReactome` - Plant Reactome
+- `SIGNOR` - SIGNOR
+- `SignaLink` - SignaLink
+
+## Enzyme and Metabolism
+
+- `EC` - Enzyme Commission number
+- `BRENDA` - BRENDA enzyme database
+- `SABIO-RK` - SABIO-RK (biochemical reactions)
+- `MetaCyc` - MetaCyc
+
+## Disease and Phenotype Databases
+
+- `OMIM` - Online Mendelian Inheritance in Man
+- `MIM` - MIM (same as OMIM)
+- `OrphaNet` - Orphanet (rare diseases)
+- `DisGeNET` - DisGeNET
+- `MalaCards` - MalaCards
+- `CTD` - Comparative Toxicogenomics Database
+- `OpenTargets` - Open Targets
+
+## Drug and Chemical Databases
+
+- `ChEMBL` - ChEMBL
+- `DrugBank` - DrugBank
+- `DrugCentral` - DrugCentral
+- `GuidetoPHARMACOLOGY` - Guide to Pharmacology
+- `SwissLipids` - SwissLipids
+
+## Gene Expression Databases
+
+- `Bgee` - Bgee gene expression
+- `ExpressionAtlas` - Expression Atlas
+- `Genevisible` - Genevisible
+- `CleanEx` - CleanEx
+
+## Proteomics Databases
+
+- `PRIDE` - PRIDE proteomics
+- `PeptideAtlas` - PeptideAtlas
+- `ProteomicsDB` - ProteomicsDB
+- `CPTAC` - CPTAC
+- `jPOST` - jPOST
+- `MassIVE` - MassIVE
+- `MaxQB` - MaxQB
+- `PaxDb` - PaxDb
+- `TopDownProteomics` - Top Down Proteomics
+
+## Protein-Protein Interaction
+
+- `STRING` - STRING
+- `BioGRID` - BioGRID
+- `IntAct` - IntAct
+- `MINT` - MINT
+- `DIP` - Database of Interacting Proteins
+- `ComplexPortal` - Complex Portal
+
+## Ontologies
+
+- `GO` - Gene Ontology
+- `GeneTree` - Ensembl GeneTree
+- `HOGENOM` - HOGENOM
+- `HOVERGEN` - HOVERGEN
+- `KO` - KEGG Orthology
+- `OMA` - OMA orthology
+- `OrthoDB` - OrthoDB
+- `TreeFam` - TreeFam
+
+## Other Specialized Databases
+
+### Glycosylation
+- `GlyConnect` - GlyConnect
+- `GlyGen` - GlyGen
+
+### Protein Modifications
+- `PhosphoSitePlus` - PhosphoSitePlus
+- `iPTMnet` - iPTMnet
+
+### Antibodies
+- `Antibodypedia` - Antibodypedia
+- `DNASU` - DNASU
+
+### Protein Localization
+- `COMPARTMENTS` - COMPARTMENTS
+- `NeXtProt` - NeXtProt (human proteins)
+
+### Evolution and Phylogeny
+- `eggNOG` - eggNOG
+- `GeneTree` - Ensembl GeneTree
+- `InParanoid` - InParanoid
+
+### Technical Resources
+- `PRO` - Protein Ontology
+- `GenomeRNAi` - GenomeRNAi
+- `PubMed` - PubMed literature references
+
+## Common Mapping Scenarios
+
+### Example 1: UniProt to PDB
+```python
+from_db = "UniProtKB_AC-ID"
+to_db = "PDB"
+ids = ["P01308", "P04637"]
+```
+
+### Example 2: Gene Name to UniProt
+```python
+from_db = "Gene_Name"
+to_db = "UniProtKB"
+ids = ["BRCA1", "TP53", "INSR"]
+```
+
+### Example 3: UniProt to Ensembl
+```python
+from_db = "UniProtKB_AC-ID"
+to_db = "Ensembl"
+ids = ["P12345"]
+```
+
+### Example 4: RefSeq to UniProt
+```python
+from_db = "RefSeq_Protein"
+to_db = "UniProtKB"
+ids = ["NP_000207.1"]
+```
+
+### Example 5: UniProt to GO Terms
+```python
+from_db = "UniProtKB_AC-ID"
+to_db = "GO"
+ids = ["P01308"]
+```
+
+## Usage Notes
+
+1. **Database names are case-sensitive**: Use exact names as listed
+
+2. **Many-to-many mappings**: One ID may map to multiple target IDs
+
+3. **Failed mappings**: Some IDs may not have mappings; check the `failedIds` field in results
+
+4. **Batch size limit**: Maximum 100,000 IDs per job
+
+5. **Result expiration**: Results are stored for 7 days
+
+6. **Bidirectional mapping**: Most databases support mapping in both directions
+
+## API Endpoints
+
+### Get available databases
+```
+GET https://rest.uniprot.org/configure/idmapping/fields
+```
+
+### Submit mapping job
+```
+POST https://rest.uniprot.org/idmapping/run
+Content-Type: application/x-www-form-urlencoded
+
+from={from_db}&to={to_db}&ids={comma_separated_ids}
+```
+
+### Check job status
+```
+GET https://rest.uniprot.org/idmapping/status/{jobId}
+```
+
+### Get results
+```
+GET https://rest.uniprot.org/idmapping/results/{jobId}
+```
+
+## Resources
+
+- ID Mapping tool: https://www.uniprot.org/id-mapping
+- API documentation: https://www.uniprot.org/help/id_mapping
+- Programmatic access: https://www.uniprot.org/help/api_idmapping