XBio:D Data Management
xBio:D Data Management
This section provides instructions on performing common data management tasks on the xBio:D database that are not privy to general users. These tasks are not available through web applications and must either be performed by running a script or a database procedure.
Change Occurrence Record (Specimen) CUID
In the Oracle SQL Developer, turn DBMS_OUTPUT on, then run the procedure EXEC updateSpmID(old_cuid, new_cuid);. The procedure will only produce output when a problem occurred.
Merged/Remove Locality Name
In the Oracle SQL Developer, turn DBMS_OUTPUT on, then run the procedure EXEC change_locality(obsolete_loc_name, valid_loc_name);. The procedure removes the obsolete locality and places all of the occurrence records from the obsolete locality into the valid locality name. There is also an additional, optional parameter coll_date, which accepts the format DD-MON-YYYY, that will change the functioning of this procedure to change only those occurrence records that were collected on that particular date. If all of the occurrences were collected on that day, the locality is removed. The procedure will only produce output when a problem occurred.
Aggregation Update
Many DB queries use tables that are aggregated from many separate tables to speed up processing. These aggregation tasks are performed automatically every Saturday under the DB job named aggregation_update. These tasks include the following:
- processDescriberIDs - Goes through each taxonomic concept that does not already have a describer specified within the Protonym table and attempts to infer from an original description or replacement name literature annotation the author of the taxon. If a match is found, then the individual describer or describer party is added to the Protonym table.
- update_people_stats - Builds the AGGR_Person_Stats table that contains the # of occurrences collected, # of papers published, # of determinations made, # of distinct events collected, and the total # of contributions for each person.
- update_genera_stats - Builds the AGGR_Genus_Stats table that contains the # of occurrences determined, # of papers published, # of images taken, # of collections deposited, and distinct events collected for each tnuid.
- update_place_children - Builds the AGGR_Place_Children table that contains a place along with each subordinate place at any lower position within the geopolitical hierarchy.
- update_taxon_children - Builds the AGGR_Taxon_Children table that contains a tnuid along with each subordinate tnuid at any lower position within the taxonomic hierarchy. Species-group taxa are excluded as parent taxa within this table.
- update_fossil_taxa - Builds the AGGR_Fossil_Taxa table that contains a tcid for each taxon concept that is a fossil. Fossil status is only applied to species-group taxa, so this procedure also added taxa in which all of its subordinate taxa are fossils.
- update_recordings - Builds the AGGR_Taxon_Recordings table that contains a tnuid and recording info id for any recording that is contained within the taxon.
- update_images - Builds the AGGR_Taxon_Images table that contains a tnuid and image id for any specimen or taxon image that is contained within the taxon. Species-group taxa are excluded as parent taxa within this table.
- update_habitats - Builds the AGGR_Habitat table that contains a tnuid and habitat for any occurrence that is contained within the taxon. Species-group taxa are excluded as parent taxa within this table.
- update_taxon_contributors - Builds the AGGR_Taxon_Contribs table that contains a tnuid, contributor, and contribution flags for every contribution from the contributor within the taxon. Species-group taxa are excluded as parent taxa within this table.
- update_inst_tcids - Builds the AGGR_Inst_Tcids table that contains the tcids for every collection where an occurrence is present. Species-group taxa are excluded as parent taxa within this table.
- update_associations - Builds the AGGR_Taxon_Assocs table that contains a tnuid and associated tnuid for every taxon that is contained within the taxon. Species-group taxa are excluded as parent taxa within this table.
