/* Copyright (C) 2008 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ /* Routines to get data from relational version of * SwissProt database. This database is generated * from SwissProt flat files by the spToDb program. * * Most of the routines take the primary SwissProt accession * as input, and will abort if this is not found in the database. * Use spIsPrimaryAcc to check for existence first if you want * to avoid this. The routines that return strings need them * free'd when you are done, and the routines that return lists * need them spFreeList'd when done unless you don't mind memory * leaks. */ #ifndef SPDB_H #define SPDB_H #ifndef JKSQL_H #include "jksql.h" #endif #define UNIPROT_DB_NAME "uniProt" #define PROTEOME_DB_NAME "proteome" typedef char SpAcc[20]; /* Enough space for accession and 0 terminator. */ struct spFeature /* A swissProt feature - that is an annotation attatched to * part of a protein. */ { struct spFeature *next; int start; /* Start coordinate (zero-based) */ int end; /* End coordinate (non-inclusive) */ int featureClass; /* ID of featureClass */ int featureType; /* ID of featureType */ char softEndBits;/* 1 for start <, 2 for start ?, 4 for end >, 8 for end ? */ }; #define spFeatureStartLess 1 #define spFeatureStartFuzzy 2 #define spFeatureEndGreater 4 #define spFeatureEndFuzzy 8 struct spCitation /* A SwissProt citation of a reference. Generally * you'll just grab the reference id out of this. * If you love SwissProt RP and RC lines you might use * the other fields. */ { struct spCitation *next; int id; /* Database (not SwissProt) ID */ SpAcc acc; /* SwissProt accession. */ int reference; /* ID in reference table. */ int rp; /* Id in rp table. */ }; boolean spIsPrimaryAcc(struct sqlConnection *conn, char *acc); /* Return TRUE if this is a primary accession in database. */ char *spFindAcc(struct sqlConnection *conn, char *id); /* Return primary accession given either display ID, * primary accession, or secondary accession. Return * NULL if not found. */ char *spAnyAccToId(struct sqlConnection *conn, char *acc); char *spAccToId(struct sqlConnection *conn, char *acc); /* Convert primary accession to SwissProt ID (which will * often look something like HXA1_HUMAN. */ char *spIdToAcc(struct sqlConnection *conn, char *id); /* Convert SwissProt ID (things like HXA1_HUMAN) to * accession. Returns NULL if the conversion fails. * (doesn't abort). */ char *spLookupPrimaryAccMaybe(struct sqlConnection *conn, char *anyAcc); /* Primary or secondary accession. */ /* This will return the primary accession. It's ok to pass in * either a primary or secondary accession. Return NULL if * not found. */ char *spLookupPrimaryAcc(struct sqlConnection *conn, char *anyAcc); /* Primary or secondary accession. */ /* This will return the primary accession. It's ok to pass in * either a primary or secondary accession. ErrAbort if * not found */ char *spDescription(struct sqlConnection *conn, char *acc); /* Return protein description. FreeMem this when done. */ boolean spIsCurated(struct sqlConnection *conn, char *acc); /* Return TRUE if it is a curated entry. */ int spAaSize(struct sqlConnection *conn, char *acc); /* Return number of amino acids. */ int spMolWeight(struct sqlConnection *conn, char *acc); /* Return molecular weight in daltons. */ char *spCreateDate(struct sqlConnection *conn, char *acc); /* Return creation date in YYYY-MM-DD format. FreeMem * this when done. */ char *spSeqDate(struct sqlConnection *conn, char *acc); /* Return sequence last update date in YYYY-MM-DD format. FreeMem * this when done. */ char *spAnnDate(struct sqlConnection *conn, char *acc); /* Return annotation last update date in YYYY-MM-DD format. FreeMem * this when done. */ char *spOrganelle(struct sqlConnection *conn, char *acc); /* Return text description of organelle. FreeMem this when done. * This may return NULL if it's not an organelle. */ struct slName *spGeneToAccs(struct sqlConnection *conn, char *gene, int taxon); /* Get list of accessions associated with this gene. If * taxon is zero then this will return all accessions, if * taxon is non-zero then it will restrict it to a single * organism with that taxon ID. */ struct slName *spGenes(struct sqlConnection *conn, char *acc); /* Return list of genes associated with accession */ struct slName *spTaxons(struct sqlConnection *conn, char *acc); /* Return list of taxons associated with accession */ struct slName *spBinomialNames(struct sqlConnection *conn, char *acc); /* Return list of scientific names of organisms * associated with accessoin */ int spTaxon(struct sqlConnection *conn, char *acc); /* Return taxon of first organism associated with accession. */ int spBinomialToTaxon(struct sqlConnection *conn, char *name); /* Return taxon associated with binomial (Mus musculus) name. */ int spCommonToTaxon(struct sqlConnection *conn, char *commonName); /* Return taxon ID associated with common (mouse) name or * binomial name. */ char *spTaxonToBinomial(struct sqlConnection *conn, int taxon); /* Return Latin binomial name associated with taxon. */ char *spTaxonToCommon(struct sqlConnection *conn, int taxon); /* Given NCBI common ID return first common name associated * with it if possible, otherwise return scientific name. */ struct slName *spKeywords(struct sqlConnection *conn, char *acc); /* Return list of keywords for accession. */ struct slName *spKeywordSearch(struct sqlConnection *conn, char *keyword, int taxon); /* Return list of accessions that use keyword. If taxon is non-zero * then restrict accessions to given organism. */ struct slName *slComments(struct sqlConnection *conn, char *acc, /* Primary accession. */ char *type); /* Comment type name, NULL for all comments. */ /* Get list of comments associated with accession. * If optional type parameter is included it should be * something in the commentType table. Some good types * are: DISEASE, FUNCTION, "SUBCELLULAR LOCATION" etc. */ struct slName *slCommentTypes(struct sqlConnection *conn); /* Get list of comment types in database. */ char *spCommentType(struct sqlConnection *conn, int typeId); /* Look up text associated with typeId. freeMem result when done. */ char *spCommentVal(struct sqlConnection *conn, int valId); /* Look up text associated with valId. freeMem result when done. */ struct slName *spExtDbAcc1List(struct sqlConnection *conn, char *acc, char *db); /* Get list of accessions from external database associated with this * swissProt entity. The db parameter can be anything in the * extDb table. Some common external databases are 'EMBL' 'PDB' 'Pfam' * 'Interpro'. */ struct slName *spEmblAccs(struct sqlConnection *conn, char *acc); /* Get list of EMBL/Genbank mRNAaccessions associated with this. */ struct slName *spPdbAccs(struct sqlConnection *conn, char *acc); /* Get list of PDB associations associated with this. */ char *spAccFromEmbl(struct sqlConnection *conn, char *acc); /* Get SwissProt accession associated with EMBL mRNA. */ struct spFeature *spFeatures(struct sqlConnection *conn, char *acc, int classId, /* Feature class ID, 0 for all */ int typeId); /* Feature type ID, 0 for all */ /* Get feature list. slFreeList this when done. */ char *spFeatureTypeName(struct sqlConnection *conn, int featureType); /* Return name associated with featureType */ int spFeatureTypeId(struct sqlConnection *conn, char *name); /* Return feature type id associated with given name. */ char *spFeatureClassName(struct sqlConnection *conn, int featureClass); /* Return name associated with featureClass. */ int spFeatureClassId(struct sqlConnection *conn, char *name); /* Return feature class id associated with given name. */ struct spCitation *spCitations(struct sqlConnection *conn, char *acc); /* Get list of citations to references associated with this * accession. You can slFreeList this when done. */ char *spRefTitle(struct sqlConnection *conn, int refId); /* Get title of reference. This can be NULL legitimately. */ struct slName *spRefAuthors(struct sqlConnection *conn, int refId); /* Get list of authors associated with reference. */ char *spRefCite(struct sqlConnection *conn, int refId); /* Get journal/page/etc of reference. */ char *spRefPubMed(struct sqlConnection *conn, int refId); /* Get PubMed id. May be NULL legitimately. */ struct slName *spRefToAccs(struct sqlConnection *conn, int refId); /* Get list of accessions associated with reference. */ char *oldSpDisplayId(char *newSpDisplayId); /* Convert from new Swiss-Prot display ID to old display ID */ char *newSpDisplayId(char *oldSpDisplayId); /* Convert from old Swiss-Prot display ID to new display ID */ char *uniProtFindPrimAcc(char *id); /* Return primary accession given an alias. */ char *uniProtFindPrimAccFromGene(char *gene, char *db); /* Return primary accession given gene name. * NULL if not found. */ struct slName *spProteinEvidence(struct sqlConnection *conn, char *acc); /* Get list of evidence that protein exists for accession. There will be at least one. */ #endif /* SPDB_H */