File: docs/single-entry.md

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docs/single-entry.md

File:	`docs/single-entry.md`
Role:	Auxiliary data
Content type:	`text/markdown`
Description:	Auxiliary data
Class:	Uniprot PHP Class Access a UniProt Protein sequence REST API.
Author:	By Saurabh Gayali
Last change:
Date:	2 months ago
Size:	`5,804 bytes`

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Single Entry Retrieval

Retrieve individual UniProtKB entries by accession number.

Endpoint

GET https://rest.uniprot.org/uniprotkb/{accession}

Basic Usage

use UniProtPHP\Http\HttpClientFactory;
use UniProtPHP\UniProt\UniProtEntry;

$httpClient = HttpClientFactory::create();
$entry = new UniProtEntry($httpClient);

$protein = $entry->get('P12345');

Response Structure

The response includes rich protein information:

[
    'primaryAccession' => 'P12345',
    'uniProtkbId' => 'AATM_RABIT',
    'organism' => [
        'scientificName' => 'Oryctolagus cuniculus',
        'commonName' => 'Rabbit',
        'taxonId' => 9986
    ],
    'proteinDescription' => [
        'recommendedName' => [
            'fullName' => ['value' => 'Aspartate aminotransferase, mitochondrial']
        ]
    ],
    'sequence' => [
        'value' => 'MALLHSARV...',
        'length' => 430,
        'molWeight' => 47409
    ],
    'comments' => [...],  // Function, catalytic activity, cofactors, etc.
    'features' => [...],  // Binding sites, modified residues, etc.
    'references' => [...]
]

Output Formats

JSON (Default)

$protein = $entry->get('P12345', 'json');
// Returns parsed PHP array

FASTA

$fasta = $entry->get('P12345', 'fasta');
echo $fasta['body'];
// Output:
// >sp|P12345|AATM_RABIT Aspartate aminotransferase, mitochondrial...
// MALLHSARVLSGVASAFHPGLAAAASARASSWWAHVEMGPPDPILGVTEAYKR...

XML

$xml = $entry->get('P12345', 'xml');
echo $xml['body'];

Tab-separated Values (TXT)

$txt = $entry->get('P12345', 'txt');
echo $txt['body'];

GFF

$gff = $entry->get('P12345', 'gff');
echo $gff['body'];

Retrieve Specific Fields

Only fetch the fields you need to reduce bandwidth:

$data = $entry->getWithFields('P12345', [
    'accession',           // Primary accession
    'protein_name',        // Protein names
    'organism_name',       // Organism
    'sequence',            // Amino acid sequence
    'cc_function',         // Function comment
    'ft_active_site',      // Active site features
    'xref_pdb'            // PDB cross-references
]);

Available Fields

Identification: - accession - Primary accession - id - Entry name - gene_names - Gene names - organism_name - Species name - organism_id - Taxonomy ID

Sequence: - sequence - Amino acid sequence - length - Sequence length - mass - Molecular weight - fragment - Is fragment?

Function: - cc_function - Function description - ec - EC number - cc_catalytic_activity - Catalytic activity - cc_cofactor - Cofactor information

Structure: - ft_binding - Binding sites - ft_active_site - Active site - ft_domain - Protein domains

Cross-references: - xref_pdb - 3D structures - xref_interpro - InterPro domains - xref_kegg - KEGG pathways

See UniProt documentation for complete field list.

Batch Retrieval

$results = $entry->getBatch([
    'P12345',
    'P00750',
    'P05067'
]);

foreach ($results as $result) {
    if (isset($result['error'])) {
        echo "Error for {$result['accession']}: {$result['error']}\n";
    } else {
        echo $result['primaryAccession'] . "\n";
    }
}

Check Entry Existence

if ($entry->exists('P12345')) {
    $protein = $entry->get('P12345');
} else {
    echo "Entry not found\n";
}

Error Handling

use UniProtPHP\Exception\UniProtException;

try {
    $protein = $entry->get('INVALID');
} catch (UniProtException $e) {
    // Entry not found (404)
    if ($e->getHttpStatus() === 404) {
        echo "Protein not in UniProtKB\n";
    }
    
    // Other HTTP errors
    else if ($e->getHttpStatus() >= 400) {
        echo "Request error: " . $e->getDetailedMessage() . "\n";
    }
    
    // Network/transport errors
    else {
        echo "Connection error: " . $e->getMessage() . "\n";
    }
}

Common Use Cases

Get Protein Function

$data = $entry->getWithFields('P12345', ['cc_function']);
foreach ($data['comments'] as $comment) {
    if ($comment['commentType'] === 'FUNCTION') {
        echo $comment['texts'][0]['value'];
    }
}

Get Subcellular Location

$data = $entry->getWithFields('P12345', ['cc_subcellular_location']);
foreach ($data['comments'] as $comment) {
    if ($comment['commentType'] === 'SUBCELLULAR LOCATION') {
        foreach ($comment['subcellularLocations'] as $location) {
            echo $location['location']['value'] . "\n";
        }
    }
}

Get GO Annotations

$data = $entry->getWithFields('P12345', ['go', 'go_id']);
foreach ($data['uniProtKBCrossReferences'] as $ref) {
    if ($ref['database'] === 'GO') {
        echo $ref['id'] . "\n";
    }
}

Get PDB Structures

$data = $entry->getWithFields('P12345', ['xref_pdb']);
foreach ($data['uniProtKBCrossReferences'] as $ref) {
    if ($ref['database'] === 'PDB') {
        echo $ref['id'] . "\n";
    }
}