Index

Symbols

--at pysec2pri-update-ids command line option pysec2pri-update-labels command line option --cache-dir pysec2pri-chebi-ids command line option pysec2pri-chebi-labels command line option pysec2pri-ensembl-ids command line option pysec2pri-ensembl-labels command line option pysec2pri-hgnc-ids command line option pysec2pri-hgnc-labels command line option pysec2pri-ncbi-ids command line option pysec2pri-ncbi-labels command line option pysec2pri-uniprot-ids command line option pysec2pri-vgnc-ids command line option pysec2pri-vgnc-labels command line option --complete pysec2pri-hgnc-ids command line option pysec2pri-hgnc-labels command line option pysec2pri-vgnc-ids command line option pysec2pri-vgnc-labels command line option --compounds pysec2pri-chebi-ids command line option pysec2pri-chebi-labels command line option --consolidate pysec2pri-chebi-ids command line option pysec2pri-chebi-labels command line option pysec2pri-ensembl-ids command line option pysec2pri-ensembl-labels command line option pysec2pri-hgnc-ids command line option pysec2pri-hgnc-labels command line option pysec2pri-ncbi-ids command line option pysec2pri-ncbi-labels command line option pysec2pri-uniprot-ids command line option pysec2pri-vgnc-ids command line option pysec2pri-vgnc-labels command line option --datasource pysec2pri-diff command line option --delac-sp pysec2pri-uniprot-ids command line option --entity-type pysec2pri-update-labels command line option pysec2pri-wikidata-ids command line option pysec2pri-wikidata-labels command line option --external-synonym pysec2pri-ensembl-labels command line option --force pysec2pri-chebi-ids command line option pysec2pri-chebi-labels command line option pysec2pri-ensembl-ids command line option pysec2pri-ensembl-labels command line option pysec2pri-hgnc-ids command line option pysec2pri-hgnc-labels command line option pysec2pri-ncbi-ids command line option pysec2pri-ncbi-labels command line option pysec2pri-uniprot-ids command line option pysec2pri-vgnc-ids command line option pysec2pri-vgnc-labels command line option --format pysec2pri-chebi-ids command line option pysec2pri-chebi-labels command line option pysec2pri-ensembl-ids command line option pysec2pri-ensembl-labels command line option pysec2pri-hgnc-ids command line option pysec2pri-hgnc-labels command line option pysec2pri-hmdb-metabolites-ids command line option pysec2pri-hmdb-proteins-ids command line option pysec2pri-ncbi-ids command line option pysec2pri-ncbi-labels command line option pysec2pri-uniprot-ids command line option pysec2pri-vgnc-ids command line option pysec2pri-vgnc-labels command line option pysec2pri-wikidata-ids command line option pysec2pri-wikidata-labels command line option --from-version pysec2pri-chebi-ids command line option pysec2pri-chebi-labels command line option pysec2pri-ensembl-ids command line option pysec2pri-ensembl-labels command line option pysec2pri-hgnc-ids command line option pysec2pri-hgnc-labels command line option pysec2pri-ncbi-ids command line option pysec2pri-ncbi-labels command line option pysec2pri-uniprot-ids command line option pysec2pri-vgnc-ids command line option pysec2pri-vgnc-labels command line option --gene pysec2pri-ensembl-ids command line option pysec2pri-ensembl-labels command line option --gene-history pysec2pri-ncbi-ids command line option --gene-info pysec2pri-ncbi-ids command line option pysec2pri-ncbi-labels command line option --mapping pysec2pri-update-ids command line option pysec2pri-update-labels command line option --mapping-session pysec2pri-ensembl-ids command line option --metabolites pysec2pri-hmdb-metabolites-ids command line option --names pysec2pri-chebi-labels command line option --no-progress pysec2pri-ambiguous command line option pysec2pri-chebi-ids command line option pysec2pri-chebi-labels command line option pysec2pri-ensembl-ids command line option pysec2pri-ensembl-labels command line option pysec2pri-hgnc-ids command line option pysec2pri-hgnc-labels command line option pysec2pri-hmdb-metabolites-ids command line option pysec2pri-hmdb-proteins-ids command line option pysec2pri-ncbi-ids command line option pysec2pri-ncbi-labels command line option pysec2pri-uniprot-ids command line option pysec2pri-update-ids command line option pysec2pri-update-labels command line option pysec2pri-vgnc-ids command line option pysec2pri-vgnc-labels command line option pysec2pri-wikidata-ids command line option pysec2pri-wikidata-labels command line option --output pysec2pri-ambiguous command line option pysec2pri-chebi-ids command line option pysec2pri-chebi-labels command line option pysec2pri-diff command line option pysec2pri-ensembl-ids command line option pysec2pri-ensembl-labels command line option pysec2pri-hgnc-ids command line option pysec2pri-hgnc-labels command line option pysec2pri-hmdb-metabolites-ids command line option pysec2pri-hmdb-proteins-ids command line option pysec2pri-ncbi-ids command line option pysec2pri-ncbi-labels command line option pysec2pri-uniprot-ids command line option pysec2pri-update-ids command line option pysec2pri-update-labels command line option pysec2pri-vgnc-ids command line option pysec2pri-vgnc-labels command line option pysec2pri-wikidata-ids command line option pysec2pri-wikidata-labels command line option

--proteins pysec2pri-hmdb-proteins-ids command line option --report pysec2pri-update-ids command line option pysec2pri-update-labels command line option --sec-ac pysec2pri-uniprot-ids command line option --secondary-ids pysec2pri-chebi-ids command line option --sep pysec2pri-update-ids command line option pysec2pri-update-labels command line option --show-all pysec2pri-diff command line option --species pysec2pri-ensembl-ids command line option pysec2pri-ensembl-labels command line option pysec2pri-ncbi-ids command line option pysec2pri-ncbi-labels command line option pysec2pri-update-labels command line option pysec2pri-vgnc-ids command line option pysec2pri-vgnc-labels command line option --stable-id-event pysec2pri-ensembl-ids command line option --subset pysec2pri-chebi-ids command line option pysec2pri-chebi-labels command line option pysec2pri-update-labels command line option --suffix pysec2pri-update-ids command line option pysec2pri-update-labels command line option --synonyms pysec2pri-update-ids command line option pysec2pri-update-labels command line option --synonyms-mapping pysec2pri-update-ids command line option pysec2pri-update-labels command line option --test-subset pysec2pri-wikidata-ids command line option pysec2pri-wikidata-labels command line option --to-version pysec2pri-chebi-ids command line option pysec2pri-chebi-labels command line option pysec2pri-ensembl-ids command line option pysec2pri-ensembl-labels command line option pysec2pri-hgnc-ids command line option pysec2pri-hgnc-labels command line option pysec2pri-ncbi-ids command line option pysec2pri-ncbi-labels command line option pysec2pri-uniprot-ids command line option pysec2pri-vgnc-ids command line option pysec2pri-vgnc-labels command line option --version pysec2pri command line option pysec2pri-ambiguous command line option pysec2pri-chebi-ids command line option pysec2pri-chebi-labels command line option pysec2pri-ensembl-ids command line option pysec2pri-ensembl-labels command line option pysec2pri-hgnc-ids command line option pysec2pri-hgnc-labels command line option pysec2pri-hmdb-metabolites-ids command line option pysec2pri-hmdb-proteins-ids command line option pysec2pri-ncbi-ids command line option pysec2pri-ncbi-labels command line option pysec2pri-uniprot-ids command line option pysec2pri-update-ids command line option pysec2pri-update-labels command line option pysec2pri-vgnc-ids command line option pysec2pri-vgnc-labels command line option pysec2pri-wikidata-ids command line option pysec2pri-wikidata-labels command line option --withdrawn pysec2pri-hgnc-ids command line option pysec2pri-vgnc-ids command line option --xref pysec2pri-ensembl-labels command line option pysec2pri-update-ids command line option pysec2pri-update-labels command line option --xref-file pysec2pri-update-ids command line option pysec2pri-update-labels command line option --xref-on pysec2pri-update-ids command line option pysec2pri-update-labels command line option --xref-predicate pysec2pri-update-ids command line option pysec2pri-update-labels command line option --xref-source pysec2pri-update-ids command line option pysec2pri-update-labels command line option -o pysec2pri-ambiguous command line option pysec2pri-chebi-ids command line option pysec2pri-chebi-labels command line option pysec2pri-diff command line option pysec2pri-ensembl-ids command line option pysec2pri-ensembl-labels command line option pysec2pri-hgnc-ids command line option pysec2pri-hgnc-labels command line option pysec2pri-hmdb-metabolites-ids command line option pysec2pri-hmdb-proteins-ids command line option pysec2pri-ncbi-ids command line option pysec2pri-ncbi-labels command line option pysec2pri-uniprot-ids command line option pysec2pri-update-ids command line option pysec2pri-update-labels command line option pysec2pri-vgnc-ids command line option pysec2pri-vgnc-labels command line option pysec2pri-wikidata-ids command line option pysec2pri-wikidata-labels command line option

_

_ambiguity_mode (BaseMappingSet attribute)

_primary_ids (BaseMappingSet attribute) _primary_labels (BaseMappingSet attribute)

B

BaseMappingSet (class in pysec2pri.parsers.base)

BaseParser (class in pysec2pri.parsers.base)

C

ChEBIParser (class in pysec2pri.parsers.chebi) check_chebi_release() (in module pysec2pri.download) check_ensembl_release() (in module pysec2pri.download) check_hgnc_release() (in module pysec2pri.download) check_hmdb_release() (in module pysec2pri.download) check_ncbi_release() (in module pysec2pri.download) check_release() (in module pysec2pri.download) check_uniprot_release() (in module pysec2pri.download)

CloudflareBlockedError combine_mapping_sets() (in module pysec2pri.api) compute_cardinalities() (IdMappingSet method) (LabelMappingSet method) config_package (BaseParser attribute) CONSOLIDATE_DATASOURCES (in module pysec2pri.constants) ContextSpec (class in pysec2pri.api) current_label_snapshot() (EnsemblParser method)

D

DATASOURCE pysec2pri-ambiguous command line option pysec2pri-list-versions command line option pysec2pri-update-ids command line option pysec2pri-update-labels command line option pysec2pri-validate-config command line option

DatasourceConfig (class in pysec2pri.parsers.base) default_species() (DatasourceConfig method) default_subset() (DatasourceConfig method) delac_url (UniProtParser property) download_datasource() (in module pysec2pri.download) download_datasource_with_release() (in module pysec2pri.download) download_file() (in module pysec2pri.download)

E

EnsemblParser (class in pysec2pri.parsers.ensembl)

entity_types() (WikidataParser class method) era_for() (DatasourceConfig method)

F

FILE1 pysec2pri-diff command line option FILE2 pysec2pri-diff command line option

find_ambiguous() (BaseMappingSet method) (in module pysec2pri.api) formats_for() (DatasourceConfig method)

G

generate_ids() (in module pysec2pri.api) generate_labels() (in module pysec2pri.api) generate_primary_ids() (in module pysec2pri.api)

generate_primary_labels() (in module pysec2pri.api) get_download_urls() (in module pysec2pri.download) get_file_last_modified() (in module pysec2pri.download) get_latest_release_info() (in module pysec2pri.download)

H

HGNCParser (class in pysec2pri.parsers.hgnc)

HMDBParser (class in pysec2pri.parsers.hmdb)

I

id_column (HGNCParser attribute) (VGNCParser attribute) IdMappingSet (class in pysec2pri.parsers.base)

INPUT_FILE pysec2pri-update-ids command line option pysec2pri-update-labels command line option

L

LabelMappingSet (class in pysec2pri.parsers.base) list_versions() (in module pysec2pri.api) (in module pysec2pri.download)

load_label_mapping() (in module pysec2pri.api) load_mapping() (in module pysec2pri.api) load_xref_mapping() (in module pysec2pri.api)

M

mapping_set_classes (BaseParser attribute) merged_patterns (HGNCParser attribute) model_config (DatasourceConfig attribute) module pysec2pri.api pysec2pri.constants pysec2pri.download pysec2pri.exports pysec2pri.update

N

NCBIParser (class in pysec2pri.parsers.ncbi)

P

parse() (ChEBIParser method) (EnsemblParser method) (HGNCParser method) (NCBIParser method) (UniProtParser method) (VGNCParser method) (WikidataParser method) parse_all() (EnsemblParser method) (HGNCParser method) (NCBIParser method) (VGNCParser method) (WikidataParser method) parse_from_file() (WikidataParser method) parse_label_history() (EnsemblParser method) parse_labels() (EnsemblParser method) (HGNCParser method) (NCBIParser method) (VGNCParser method) (WikidataParser method) parse_primary_ids() (ChEBIParser method) (EnsemblParser method) (HGNCParser method) (HMDBParser method) (NCBIParser method) (UniProtParser method) (VGNCParser method) parse_primary_labels() (ChEBIParser method) (EnsemblParser method) (HGNCParser method) (NCBIParser method) (VGNCParser method) parse_synonyms() (ChEBIParser method) products (DatasourceConfig attribute) pysec2pri command line option --version pysec2pri-ambiguous command line option --no-progress --output --version -o DATASOURCE pysec2pri-chebi-ids command line option --cache-dir --compounds --consolidate --force --format --from-version --no-progress --output --secondary-ids --subset --to-version --version -o pysec2pri-chebi-labels command line option --cache-dir --compounds --consolidate --force --format --from-version --names --no-progress --output --subset --to-version --version -o pysec2pri-diff command line option --datasource --output --show-all -o FILE1 FILE2 pysec2pri-ensembl-ids command line option --cache-dir --consolidate --force --format --from-version --gene --mapping-session --no-progress --output --species --stable-id-event --to-version --version -o pysec2pri-ensembl-labels command line option --cache-dir --consolidate --external-synonym --force --format --from-version --gene --no-progress --output --species --to-version --version --xref -o pysec2pri-hgnc-ids command line option --cache-dir --complete --consolidate --force --format --from-version --no-progress --output --to-version --version --withdrawn -o pysec2pri-hgnc-labels command line option --cache-dir --complete --consolidate --force --format --from-version --no-progress --output --to-version --version -o pysec2pri-hmdb-metabolites-ids command line option --format --metabolites --no-progress --output --version -o pysec2pri-hmdb-proteins-ids command line option --format --no-progress --output --proteins --version -o

pysec2pri-list-versions command line option DATASOURCE pysec2pri-ncbi-ids command line option --cache-dir --consolidate --force --format --from-version --gene-history --gene-info --no-progress --output --species --to-version --version -o pysec2pri-ncbi-labels command line option --cache-dir --consolidate --force --format --from-version --gene-info --no-progress --output --species --to-version --version -o pysec2pri-uniprot-ids command line option --cache-dir --consolidate --delac-sp --force --format --from-version --no-progress --output --sec-ac --to-version --version -o pysec2pri-update-ids command line option --at --mapping --no-progress --output --report --sep --suffix --synonyms --synonyms-mapping --version --xref --xref-file --xref-on --xref-predicate --xref-source -o DATASOURCE INPUT_FILE pysec2pri-update-labels command line option --at --entity-type --mapping --no-progress --output --report --sep --species --subset --suffix --synonyms --synonyms-mapping --version --xref --xref-file --xref-on --xref-predicate --xref-source -o DATASOURCE INPUT_FILE pysec2pri-validate-config command line option DATASOURCE pysec2pri-vgnc-ids command line option --cache-dir --complete --consolidate --force --format --from-version --no-progress --output --species --to-version --version --withdrawn -o pysec2pri-vgnc-labels command line option --cache-dir --complete --consolidate --force --format --from-version --no-progress --output --species --to-version --version -o pysec2pri-wikidata-ids command line option --entity-type --format --no-progress --output --test-subset --version -o pysec2pri-wikidata-labels command line option --entity-type --format --no-progress --output --test-subset --version -o pysec2pri.api module pysec2pri.constants module pysec2pri.download module pysec2pri.exports module pysec2pri.update module

R

ReleaseInfo (class in pysec2pri.download) resolve_ids() (in module pysec2pri.api)

resolve_labels() (in module pysec2pri.api) resolve_release_date() (in module pysec2pri.download)

S

save() (BaseMappingSet method) (IdMappingSet method) (in module pysec2pri.api) (LabelMappingSet method)

sec_ac_url (UniProtParser property) sources() (in module pysec2pri.api) species_token() (DatasourceConfig method) supports_consolidate() (in module pysec2pri.api)

T

to_json() (BaseMappingSet method) to_label_sec2pri() (LabelMappingSet method) to_name2synonym() (LabelMappingSet method) to_owl() (BaseMappingSet method)

to_pri_ids() (IdMappingSet method) to_pri_labels() (LabelMappingSet method) to_rdf() (BaseMappingSet method) to_sssom() (BaseMappingSet method)

U

UniProtParser (class in pysec2pri.parsers.uniprot)

V

version_query (DatasourceConfig attribute)

VGNCParser (class in pysec2pri.parsers.vgnc)

W

WikidataParser (class in pysec2pri.parsers.wikidata) withdrawn_label_column (HGNCParser attribute) (VGNCParser attribute) write_all_formats() (in module pysec2pri.api) write_diff_output() (in module pysec2pri.api) write_json() (in module pysec2pri.api) (in module pysec2pri.exports) write_label2prev() (in module pysec2pri.exports) write_label_sec2pri() (in module pysec2pri.api) (in module pysec2pri.exports) write_name2synonym() (in module pysec2pri.api) (in module pysec2pri.exports)

write_output() (in module pysec2pri.api) (in module pysec2pri.exports) write_owl() (in module pysec2pri.api) (in module pysec2pri.exports) write_pri_ids() (in module pysec2pri.exports) write_pri_labels() (in module pysec2pri.exports) write_rdf() (in module pysec2pri.api) (in module pysec2pri.exports) write_sec2pri() (in module pysec2pri.api) (in module pysec2pri.exports) write_secondary() (in module pysec2pri.exports) write_sssom() (in module pysec2pri.api) (in module pysec2pri.exports)

X

xref_source() (DatasourceConfig method)