Initial commit

skills/uniprot-database/references/api_examples.md

@@ -0,0 +1,413 @@
+# UniProt API Examples
+
+Practical code examples for interacting with the UniProt REST API in multiple languages.
+
+## Python Examples
+
+### Example 1: Basic Search
+```python
+import requests
+
+# Search for human insulin proteins
+url = "https://rest.uniprot.org/uniprotkb/search"
+params = {
+    "query": "insulin AND organism_id:9606 AND reviewed:true",
+    "format": "json",
+    "size": 10
+}
+
+response = requests.get(url, params=params)
+data = response.json()
+
+for result in data['results']:
+    print(f"{result['primaryAccession']}: {result['proteinDescription']['recommendedName']['fullName']['value']}")
+```
+
+### Example 2: Retrieve Protein Sequence
+```python
+import requests
+
+# Get human insulin sequence in FASTA format
+accession = "P01308"
+url = f"https://rest.uniprot.org/uniprotkb/{accession}.fasta"
+
+response = requests.get(url)
+print(response.text)
+```
+
+### Example 3: Custom Fields
+```python
+import requests
+
+# Get specific fields only
+url = "https://rest.uniprot.org/uniprotkb/search"
+params = {
+    "query": "gene:BRCA1 AND reviewed:true",
+    "format": "tsv",
+    "fields": "accession,gene_names,organism_name,length,cc_function"
+}
+
+response = requests.get(url, params=params)
+print(response.text)
+```
+
+### Example 4: ID Mapping
+```python
+import requests
+import time
+
+def map_uniprot_ids(ids, from_db, to_db):
+    # Submit job
+    submit_url = "https://rest.uniprot.org/idmapping/run"
+    data = {
+        "from": from_db,
+        "to": to_db,
+        "ids": ",".join(ids)
+    }
+
+    response = requests.post(submit_url, data=data)
+    job_id = response.json()["jobId"]
+
+    # Poll for completion
+    status_url = f"https://rest.uniprot.org/idmapping/status/{job_id}"
+    while True:
+        response = requests.get(status_url)
+        status = response.json()
+        if "results" in status or "failedIds" in status:
+            break
+        time.sleep(3)
+
+    # Get results
+    results_url = f"https://rest.uniprot.org/idmapping/results/{job_id}"
+    response = requests.get(results_url)
+    return response.json()
+
+# Map UniProt IDs to PDB
+ids = ["P01308", "P04637"]
+mapping = map_uniprot_ids(ids, "UniProtKB_AC-ID", "PDB")
+print(mapping)
+```
+
+### Example 5: Stream Large Results
+```python
+import requests
+
+# Stream all reviewed human proteins
+url = "https://rest.uniprot.org/uniprotkb/stream"
+params = {
+    "query": "organism_id:9606 AND reviewed:true",
+    "format": "fasta"
+}
+
+response = requests.get(url, params=params, stream=True)
+
+# Process in chunks
+with open("human_proteins.fasta", "w") as f:
+    for chunk in response.iter_content(chunk_size=8192, decode_unicode=True):
+        if chunk:
+            f.write(chunk)
+```
+
+### Example 6: Pagination
+```python
+import requests
+
+def get_all_results(query, fields=None):
+    """Get all results with pagination"""
+    url = "https://rest.uniprot.org/uniprotkb/search"
+    all_results = []
+
+    params = {
+        "query": query,
+        "format": "json",
+        "size": 500  # Max size per page
+    }
+
+    if fields:
+        params["fields"] = ",".join(fields)
+
+    while True:
+        response = requests.get(url, params=params)
+        data = response.json()
+        all_results.extend(data['results'])
+
+        # Check for next page
+        if 'next' in data:
+            url = data['next']
+        else:
+            break
+
+    return all_results
+
+# Get all human kinases
+results = get_all_results(
+    "protein_name:kinase AND organism_id:9606 AND reviewed:true",
+    fields=["accession", "gene_names", "protein_name"]
+)
+print(f"Found {len(results)} proteins")
+```
+
+## cURL Examples
+
+### Example 1: Simple Search
+```bash
+# Search for insulin proteins
+curl "https://rest.uniprot.org/uniprotkb/search?query=insulin&format=json&size=5"
+```
+
+### Example 2: Get Protein Entry
+```bash
+# Get human insulin in FASTA format
+curl "https://rest.uniprot.org/uniprotkb/P01308.fasta"
+```
+
+### Example 3: Custom Fields
+```bash
+# Get specific fields in TSV format
+curl "https://rest.uniprot.org/uniprotkb/search?query=gene:BRCA1&format=tsv&fields=accession,gene_names,length"
+```
+
+### Example 4: ID Mapping - Submit Job
+```bash
+# Submit mapping job
+curl -X POST "https://rest.uniprot.org/idmapping/run" \
+  -H "Content-Type: application/x-www-form-urlencoded" \
+  -d "from=UniProtKB_AC-ID&to=PDB&ids=P01308,P04637"
+```
+
+### Example 5: ID Mapping - Get Results
+```bash
+# Get mapping results (replace JOB_ID)
+curl "https://rest.uniprot.org/idmapping/results/JOB_ID"
+```
+
+### Example 6: Download All Results
+```bash
+# Download all human reviewed proteins
+curl "https://rest.uniprot.org/uniprotkb/stream?query=organism_id:9606+AND+reviewed:true&format=fasta" \
+  -o human_proteins.fasta
+```
+
+## R Examples
+
+### Example 1: Basic Search
+```r
+library(httr)
+library(jsonlite)
+
+# Search for insulin proteins
+url <- "https://rest.uniprot.org/uniprotkb/search"
+query_params <- list(
+  query = "insulin AND organism_id:9606",
+  format = "json",
+  size = 10
+)
+
+response <- GET(url, query = query_params)
+data <- fromJSON(content(response, "text"))
+
+# Extract accessions and names
+proteins <- data$results[, c("primaryAccession", "proteinDescription")]
+print(proteins)
+```
+
+### Example 2: Get Sequences
+```r
+library(httr)
+
+# Get protein sequence
+accession <- "P01308"
+url <- paste0("https://rest.uniprot.org/uniprotkb/", accession, ".fasta")
+
+response <- GET(url)
+sequence <- content(response, "text")
+cat(sequence)
+```
+
+### Example 3: Download to Data Frame
+```r
+library(httr)
+library(readr)
+
+# Get data as TSV
+url <- "https://rest.uniprot.org/uniprotkb/search"
+query_params <- list(
+  query = "gene:BRCA1 AND reviewed:true",
+  format = "tsv",
+  fields = "accession,gene_names,organism_name,length"
+)
+
+response <- GET(url, query = query_params)
+data <- read_tsv(content(response, "text"))
+print(data)
+```
+
+## JavaScript Examples
+
+### Example 1: Fetch API
+```javascript
+// Search for proteins
+async function searchUniProt(query) {
+  const url = `https://rest.uniprot.org/uniprotkb/search?query=${encodeURIComponent(query)}&format=json&size=10`;
+
+  const response = await fetch(url);
+  const data = await response.json();
+
+  return data.results;
+}
+
+// Usage
+searchUniProt("insulin AND organism_id:9606")
+  .then(results => console.log(results));
+```
+
+### Example 2: Get Protein Entry
+```javascript
+async function getProtein(accession, format = "json") {
+  const url = `https://rest.uniprot.org/uniprotkb/${accession}.${format}`;
+
+  const response = await fetch(url);
+
+  if (format === "json") {
+    return await response.json();
+  } else {
+    return await response.text();
+  }
+}
+
+// Usage
+getProtein("P01308", "fasta")
+  .then(sequence => console.log(sequence));
+```
+
+### Example 3: ID Mapping
+```javascript
+async function mapIds(ids, fromDb, toDb) {
+  // Submit job
+  const submitUrl = "https://rest.uniprot.org/idmapping/run";
+  const formData = new URLSearchParams({
+    from: fromDb,
+    to: toDb,
+    ids: ids.join(",")
+  });
+
+  const submitResponse = await fetch(submitUrl, {
+    method: "POST",
+    body: formData
+  });
+  const { jobId } = await submitResponse.json();
+
+  // Poll for completion
+  const statusUrl = `https://rest.uniprot.org/idmapping/status/${jobId}`;
+  while (true) {
+    const statusResponse = await fetch(statusUrl);
+    const status = await statusResponse.json();
+
+    if ("results" in status || "failedIds" in status) {
+      break;
+    }
+
+    await new Promise(resolve => setTimeout(resolve, 3000));
+  }
+
+  // Get results
+  const resultsUrl = `https://rest.uniprot.org/idmapping/results/${jobId}`;
+  const resultsResponse = await fetch(resultsUrl);
+  return await resultsResponse.json();
+}
+
+// Usage
+mapIds(["P01308", "P04637"], "UniProtKB_AC-ID", "PDB")
+  .then(mapping => console.log(mapping));
+```
+
+## Advanced Examples
+
+### Example: Batch Processing with Rate Limiting
+```python
+import requests
+import time
+from typing import List, Dict
+
+class UniProtClient:
+    def __init__(self, rate_limit=1.0):
+        self.base_url = "https://rest.uniprot.org"
+        self.rate_limit = rate_limit
+        self.last_request = 0
+
+    def _rate_limit(self):
+        """Enforce rate limiting"""
+        elapsed = time.time() - self.last_request
+        if elapsed < self.rate_limit:
+            time.sleep(self.rate_limit - elapsed)
+        self.last_request = time.time()
+
+    def batch_get_proteins(self, accessions: List[str],
+                          batch_size: int = 100) -> List[Dict]:
+        """Get proteins in batches"""
+        results = []
+
+        for i in range(0, len(accessions), batch_size):
+            batch = accessions[i:i + batch_size]
+            query = " OR ".join([f"accession:{acc}" for acc in batch])
+
+            self._rate_limit()
+
+            response = requests.get(
+                f"{self.base_url}/uniprotkb/search",
+                params={
+                    "query": query,
+                    "format": "json",
+                    "size": batch_size
+                }
+            )
+
+            if response.ok:
+                data = response.json()
+                results.extend(data.get('results', []))
+            else:
+                print(f"Error in batch {i//batch_size}: {response.status_code}")
+
+        return results
+
+# Usage
+client = UniProtClient(rate_limit=0.5)
+accessions = ["P01308", "P04637", "P12345", "Q9Y6K9"]
+proteins = client.batch_get_proteins(accessions)
+```
+
+### Example: Download with Progress Bar
+```python
+import requests
+from tqdm import tqdm
+
+def download_with_progress(query, output_file, format="fasta"):
+    """Download results with progress bar"""
+    url = "https://rest.uniprot.org/uniprotkb/stream"
+    params = {
+        "query": query,
+        "format": format
+    }
+
+    response = requests.get(url, params=params, stream=True)
+    total_size = int(response.headers.get('content-length', 0))
+
+    with open(output_file, 'wb') as f, \
+         tqdm(total=total_size, unit='B', unit_scale=True) as pbar:
+        for chunk in response.iter_content(chunk_size=8192):
+            f.write(chunk)
+            pbar.update(len(chunk))
+
+# Usage
+download_with_progress(
+    "organism_id:9606 AND reviewed:true",
+    "human_proteome.fasta"
+)
+```
+
+## Resources
+
+- API Documentation: https://www.uniprot.org/help/api
+- Interactive API Explorer: https://www.uniprot.org/api-documentation
+- Python client (Unipressed): https://github.com/multimeric/Unipressed
+- Bioservices package: https://bioservices.readthedocs.io/

skills/uniprot-database/references/api_fields.md

@@ -0,0 +1,275 @@
+# 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

skills/uniprot-database/references/id_mapping_databases.md

@@ -0,0 +1,285 @@
+# 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

skills/uniprot-database/references/query_syntax.md

@@ -0,0 +1,256 @@
+# UniProt Query Syntax Reference
+
+Comprehensive guide to UniProt search query syntax for constructing complex searches.
+
+## Basic Syntax
+
+### Simple Queries
+```
+insulin
+kinase
+```
+
+### Field-Specific Searches
+```
+gene:BRCA1
+accession:P12345
+organism_name:human
+protein_name:kinase
+```
+
+## Boolean Operators
+
+### AND (both terms must be present)
+```
+insulin AND diabetes
+kinase AND human
+gene:BRCA1 AND reviewed:true
+```
+
+### OR (either term can be present)
+```
+diabetes OR insulin
+(cancer OR tumor) AND human
+```
+
+### NOT (exclude terms)
+```
+kinase NOT human
+protein_name:kinase NOT organism_name:mouse
+```
+
+### Grouping with Parentheses
+```
+(diabetes OR insulin) AND reviewed:true
+(gene:BRCA1 OR gene:BRCA2) AND organism_id:9606
+```
+
+## Common Search Fields
+
+### Identification
+- `accession:P12345` - UniProt accession number
+- `id:INSR_HUMAN` - Entry name
+- `gene:BRCA1` - Gene name
+- `gene_exact:BRCA1` - Exact gene name match
+
+### Organism/Taxonomy
+- `organism_name:human` - Organism name
+- `organism_name:"Homo sapiens"` - Exact organism name (use quotes for multi-word)
+- `organism_id:9606` - NCBI taxonomy ID
+- `taxonomy_id:9606` - Same as organism_id
+- `taxonomy_name:"Homo sapiens"` - Taxonomy name
+
+### Protein Information
+- `protein_name:insulin` - Protein name
+- `protein_name:"insulin receptor"` - Exact protein name
+- `reviewed:true` - Only Swiss-Prot (reviewed) entries
+- `reviewed:false` - Only TrEMBL (unreviewed) entries
+
+### Sequence Properties
+- `length:[100 TO 500]` - Sequence length range
+- `mass:[50000 TO 100000]` - Molecular mass in Daltons
+- `sequence:MVLSPADKTNVK` - Exact sequence match
+- `fragment:false` - Exclude fragment sequences
+
+### Gene Ontology (GO)
+- `go:0005515` - GO term ID (0005515 = protein binding)
+- `go_f:* ` - Any molecular function
+- `go_p:*` - Any biological process
+- `go_c:*` - Any cellular component
+
+### Annotations
+- `annotation:(type:signal)` - Has signal peptide annotation
+- `annotation:(type:transmem)` - Has transmembrane region
+- `cc_function:*` - Has function comment
+- `cc_interaction:*` - Has interaction comment
+- `ft_domain:*` - Has domain feature
+
+### Database Cross-References
+- `xref:pdb` - Has PDB structure
+- `xref:ensembl` - Has Ensembl reference
+- `database:pdb` - Same as xref
+- `database:(type:pdb)` - Alternative syntax
+
+### Protein Families and Domains
+- `family:"protein kinase"` - Protein family
+- `keyword:"Protein kinase"` - Keyword annotation
+- `cc_similarity:*` - Has similarity comment
+
+## Range Queries
+
+### Numeric Ranges
+```
+length:[100 TO 500]          # Between 100 and 500
+mass:[* TO 50000]            # Less than or equal to 50000
+created:[2023-01-01 TO *]   # Created after Jan 1, 2023
+```
+
+### Date Ranges
+```
+created:[2023-01-01 TO 2023-12-31]
+modified:[2024-01-01 TO *]
+```
+
+## Wildcards
+
+### Single Character (?)
+```
+gene:BRCA?      # Matches BRCA1, BRCA2, etc.
+```
+
+### Multiple Characters (*)
+```
+gene:BRCA*      # Matches BRCA1, BRCA2, BRCA1P1, etc.
+protein_name:kinase*
+organism_name:Homo*
+```
+
+## Advanced Searches
+
+### Existence Queries
+```
+cc_function:*              # Has any function annotation
+ft_domain:*                # Has any domain feature
+xref:pdb                   # Has PDB structure
+```
+
+### Combined Complex Queries
+```
+# Human reviewed kinases with PDB structure
+(protein_name:kinase OR family:kinase) AND organism_id:9606 AND reviewed:true AND xref:pdb
+
+# Cancer-related proteins excluding mice
+(disease:cancer OR keyword:cancer) NOT organism_name:mouse
+
+# Membrane proteins with signal peptides
+annotation:(type:transmem) AND annotation:(type:signal) AND reviewed:true
+
+# Recently updated human proteins
+organism_id:9606 AND modified:[2024-01-01 TO *] AND reviewed:true
+```
+
+## Field-Specific Examples
+
+### Protein Names
+```
+protein_name:"insulin receptor"    # Exact phrase
+protein_name:insulin*              # Starts with insulin
+recommended_name:insulin           # Recommended name only
+alternative_name:insulin           # Alternative names only
+```
+
+### Genes
+```
+gene:BRCA1                        # Gene symbol
+gene_exact:BRCA1                  # Exact gene match
+olnName:BRCA1                     # Ordered locus name
+orfName:BRCA1                     # ORF name
+```
+
+### Organisms
+```
+organism_name:human               # Common name
+organism_name:"Homo sapiens"      # Scientific name
+organism_id:9606                  # Taxonomy ID
+lineage:primates                  # Taxonomic lineage
+```
+
+### Features
+```
+ft_signal:*                       # Signal peptide
+ft_transmem:*                     # Transmembrane region
+ft_domain:"Protein kinase"        # Specific domain
+ft_binding:*                      # Binding site
+ft_site:*                         # Any site
+```
+
+### Comments (cc_)
+```
+cc_function:*                     # Function description
+cc_catalytic_activity:*           # Catalytic activity
+cc_pathway:*                      # Pathway involvement
+cc_interaction:*                  # Protein interactions
+cc_subcellular_location:*         # Subcellular location
+cc_tissue_specificity:*           # Tissue specificity
+cc_disease:cancer                 # Disease association
+```
+
+## Tips and Best Practices
+
+1. **Use quotes for exact phrases**: `organism_name:"Homo sapiens"` not `organism_name:Homo sapiens`
+
+2. **Filter by review status**: Add `AND reviewed:true` for high-quality Swiss-Prot entries
+
+3. **Combine wildcards carefully**: `*kinase*` may be too broad; `kinase*` is more specific
+
+4. **Use parentheses for complex logic**: `(A OR B) AND (C OR D)` is clearer than `A OR B AND C OR D`
+
+5. **Numeric ranges are inclusive**: `length:[100 TO 500]` includes both 100 and 500
+
+6. **Field prefixes**: Learn common prefixes:
+   - `cc_` = Comments
+   - `ft_` = Features
+   - `go_` = Gene Ontology
+   - `xref_` = Cross-references
+
+7. **Check field names**: Use the API's `/configure/uniprotkb/result-fields` endpoint to see all available fields
+
+## Query Validation
+
+Test queries using:
+- **Web interface**: https://www.uniprot.org/uniprotkb
+- **API**: https://rest.uniprot.org/uniprotkb/search?query=YOUR_QUERY
+- **API documentation**: https://www.uniprot.org/help/query-fields
+
+## Common Patterns
+
+### Find well-characterized proteins
+```
+reviewed:true AND xref:pdb AND cc_function:*
+```
+
+### Find disease-associated proteins
+```
+cc_disease:* AND organism_id:9606 AND reviewed:true
+```
+
+### Find proteins with experimental evidence
+```
+existence:"Evidence at protein level" AND reviewed:true
+```
+
+### Find secreted proteins
+```
+cc_subcellular_location:secreted AND reviewed:true
+```
+
+### Find drug targets
+```
+keyword:"Pharmaceutical" OR keyword:"Drug target"
+```
+
+## Resources
+
+- Full query field reference: https://www.uniprot.org/help/query-fields
+- API query documentation: https://www.uniprot.org/help/api_queries
+- Text search documentation: https://www.uniprot.org/help/text-search