
Changes in version 1.0.13:

USER VISIBLE CHANGES

    o   Update annotations to PANTHER 19.0 and pathways 3.6.8, preserving
        the SQLite schema and exported query API.
    o   Host the versioned SQLite resource on Zenodo under DOI
        10.5281/zenodo.22729518; AnnotationHub continues to provide discovery,
        download and local caching as resource AH122304.
    o   Reuse the maintainer's UniProt-to-Entrez mapping snapshot from
        2023-09-20; the historical file's UniProt release was not recorded.
    o   Correct organism assignment in the shared green_algae source file:
        CHLRE and KLENI proteins are now assigned from each record's species ID.
    o   Include all 144 source organisms, including ENTH1 and XENLA.
        Upstream BRACM and TRIV3 replace BRARP and TRIVA with different
        taxonomy IDs. Preserve the ASHGO package key for renamed EREGS
        because its taxonomy ID remains 284811.
    o   Correct genome-source metadata, preserve complete UniProt accessions,
        and check all downloads against recorded checksums.
    o   Update offline test references from independent v19 sources.
        Retain separate raw and ontology-normalized live API comparisons.

BUILD CHANGES

    o   Replace obsolete FTP/HTML acquisition with checked HTTPS sources.
        Speed up large joins and ontology traversal without changing the schema.
    o   Build a separate candidate database; do not overwrite previous releases.

Changes in version 1.0.12:

USER VISIBLE CHANGES

    o   db updated to PANTHER release v18.0


Changes in version 1.0.11:

USER VISIBLE CHANGES

    o   db updated to PANTHER release v16.0 including new species


Changes in version 1.0.10:

USER VISIBLE CHANGES

    o   db updated to PANTHER release v14.1 including new species
    o   sqlite database moved to AnnotationHub
    o   entrez db updated based on uniprot to entrez id mappings to include the latest entrez id to panther family id mappings
    o   to limit the output, select queries now return only INNER joins hence dropping results with no FAMILY_ID association
    o   left join can be enforced using argument jointype="left" in select query


Changes in version 1.0.4:

NO USER VISIBLE CHANGES

    o   db updated to PANTHER release v12.0
    o   added all species available on http://pantherdb.org


Changes in version 1.0.3:

NO USER VISIBLE CHANGES


Changes in version 1.0.2:

USER VISIBLE CHANGES

    o   db updated to PANTHER release v10.0
    o   rename of organism related methods: species(), availableSpecies() and resetSpecies() are now called pthOrganisms(), availablePthOrganisms() and resetPthOrganisms(). Functionality is unchanged.


Changes in version 1.0.1:

USER VISIBLE CHANGES

    o   PANTHER.db is now using RSQLite v1.0 compliant code


Changes in version 1.0.0:

USER VISIBLE CHANGES

    o   db updated to PANTHER release v9.0
    o   fixed a bug preventing COMPONENT_TERM queries
    o   fixed a file permission bug
    o   select queries will now return outer joins instead of inner joints i.e. incomplete results are allowed
    o   species pre selection will strictly limit information from joined tables to information related to the selected species.
