biocontext_kb.core.pride

biocontext_kb.core.pride#

Functions#

get_pride_project(project_accession[, include_files, ...])

Retrieve detailed information about a specific PRIDE mass spectrometry proteomics project. Returns metadata and experimental details.

search_pride_projects([keyword, organism_filter, ...])

Search PRIDE database for mass spectrometry proteomics projects using keywords and filters.

search_pride_proteins(project_accession[, keyword, ...])

Search for proteins identified in a specific PRIDE mass spectrometry project. Useful for finding specific proteins in proteomics datasets.

Package Contents#

biocontext_kb.core.pride.get_pride_project(project_accession, include_files=False, include_similar_projects=False)#

Retrieve detailed information about a specific PRIDE mass spectrometry proteomics project. Returns metadata and experimental details.

Returns:

Project details with accession, title, description, organisms, instruments, publications, optionally files/similar_projects or error message.

Return type:

dict

Parameters:

  • project_accession (Annotated[str, Field(description="PRIDE project accession (e.g., 'PRD000001')")])

  • include_files (Annotated[bool, Field(description='Include file information (limited to first 20 files)')])

  • include_similar_projects (Annotated[bool, Field(description='Include similar projects based on metadata (limited to 10)')])

biocontext_kb.core.pride.search_pride_projects(keyword=None, organism_filter=None, instrument_filter=None, experiment_type_filter=None, page_size=20, sort_field='submissionDate', sort_direction='DESC')#

Search PRIDE database for mass spectrometry proteomics projects using keywords and filters.

Returns:

Results array with project accessions, titles, descriptions, organisms, instruments, experiment types, count, search_criteria or error message.

Return type:

dict

Parameters:

  • keyword (Annotated[Optional[str], Field(description="Search keywords (e.g., 'proteome', 'cancer', 'human')")])

  • organism_filter (Annotated[Optional[str], Field(description="Organism filter (e.g., 'Homo sapiens', 'human')")])

  • instrument_filter (Annotated[Optional[str], Field(description="Instrument type filter (e.g., 'Orbitrap', 'LTQ')")])

  • experiment_type_filter (Annotated[Optional[str], Field(description="Experiment type filter (e.g., 'TMT', 'Label-free')")])

  • page_size (Annotated[int, Field(description='Number of results to return (max 100)')])

  • sort_field (Annotated[str, Field(description='Sort field: submissionDate or publicationDate')])

  • sort_direction (Annotated[str, Field(description='Sort direction: ASC or DESC')])

biocontext_kb.core.pride.search_pride_proteins(project_accession, keyword=None, page_size=20, sort_field='accession', sort_direction='ASC')#

Search for proteins identified in a specific PRIDE mass spectrometry project. Useful for finding specific proteins in proteomics datasets.

Returns:

Proteins list with accessions, names, genes, sequences, modifications, associated projects or error message.

Return type:

dict

Parameters:

  • project_accession (Annotated[str, Field(description='PRIDE project accession to search proteins in')])

  • keyword (Annotated[Optional[str], Field(description='Search keyword for protein names or accessions')])

  • page_size (Annotated[int, Field(description='Number of results to return (max 100)')])

  • sort_field (Annotated[str, Field(description='Sort field: accession, proteinName, or gene')])

  • sort_direction (Annotated[str, Field(description='Sort direction: ASC or DESC')])

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