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Germplasm Clearing House Mechanism (PROTOTYPE)
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Data model

uddi_entity

CREATE TABLE uddi_entity ( uddi_id serial NOT NULL, entity_name character varying(255), discovery_url character varying(255) NOT NULL, provider_url character varying(255), provider_dsa character varying(50), provider_gbif_key character varying(255), provider_institute_id integer, provider_person_id integer, provider_institute_name character varying(255), provider_institute_acronym character varying(255), provider_institute_url character varying(255), provider_person_name character varying(255), provider_email character varying(255), source_institute_id integer, source_person_id integer, source_institute_name character varying(255), source_institute_acronym character varying(255), source_institute_url character varying(255), source_person_name character varying(255), source_person_url character varying(255), source_email character varying(255), description text, remarks text, credtm timestamp(0) without time zone DEFAULT now(), creusr character varying(32) DEFAULT current_user, upddtm timestamp(0) without time zone DEFAULT now(), updusr character varying(32) DEFAULT current_user )
Index of Germplasm BioCASE web services, dsa. This is the registered BioCASE web service entry point. Used to probe a harvest instance

uddi_ping

CREATE TABLE uddi_ping ( uddi_ping_id serial NOT NULL, uddi_id integer, provider_dsa character varying(255), ping_url character varying(255), ping_result character varying(255), ping_ms float, remarks text, creusr character varying(100) DEFAULT CURRENT_USER, credtm timestamp(0) without time zone DEFAULT now() )
Ping results, access log for remote BioCASE server

mapped_concepts

CREATE TABLE mapped_concepts ( map_id serial NOT NULL, uddi_id integer NOT NULL, schema_id integer, concept_id integer, schema_namespace character varying(255), concept_xpath character varying(255), concept_datatype character varying(255), concept_searchable character varying(255), creusr character varying(100) DEFAULT CURRENT_USER, credtm timestamp(0) without time zone DEFAULT now() )
Index of the mapped concepts from each data provider (uddi entity)

harvest_log

CREATE TABLE harvest_log ( harvest_id serial NOT NULL, uddi_id integer, schema_id integer, provider_url character varying(255), schema_namespace character varying(255), num_records integer, page_records integer, harvested_records integer, harvest_duration float, harvest_dtm timestamp(0) without time zone, harvest_result character varying(255), remarks text, creusr character varying(100) DEFAULT CURRENT_USER, credtm timestamp(0) without time zone DEFAULT now() )
Log of data harvest events, settings, records retrieved, harvest duration time etc.

data_schema

CREATE TABLE data_schema ( schema_id serial NOT NULL, schema_namespace character varying(255), schema_name character varying(255), schema_title character varying(255), schema_version character varying(32), schema_url character varying(255), record_identifier character varying(255), xpath_unit_id character varying(255), published character varying(20), release_notes text, schema_description text, schema_remarks text, credtm timestamp(0) without time zone DEFAULT now(), creusr character varying(32), upddtm timestamp(0) without time zone DEFAULT now(), updusr character varying(32) )
Index of supported data schema (CHM).

data_concept

CREATE TABLE data_concept ( concept_id serial NOT NULL, concept_name character varying(255), concept_xpath character varying(255), concept_type character varying(255), min integer, max integer, schema_id integer NOT NULL, schema_namespace character varying(255), concept_description text, concept_remarks text, credtm timestamp(0) without time zone DEFAULT now(), creusr character varying(32), upddtm timestamp(0) without time zone DEFAULT now(), updusr character varying(32) )
Index of data elements/concepts from the XML schema (CHM).

germplasm

CREATE TABLE germplasm ( germplasm_id serial NOT NULL, accession_guid character varying(255), accession_local_id character varying(255), accession_name character varying(255), biological_status_code character varying(3), biological_status character varying(100), holding_institute character varying(255), holding_institute_code character varying(6), collection_name character varying(255), acquisition_date character varying(10), acquisition_source character varying(2), storage_code character varying(2), accession_url character varying(255), accession_last_modified character varying(255), accession_remarks text, other_accession_id character varying(255), safe_institute character varying(255), safe_institute_code character varying(6), donor_institute character varying(255), donor_institute_code character varying(6), donor_accession_id character varying(255), longitude float, longitude_string character varying(8), latitude float, latitude_string character varying(7), coordinate_inaccuracy integer, geodetic_datum character varying(255), elevation integer, collecting_place character varying(255), collecting_country character varying(255), collecting_country_code character varying(3), collecting_date character varying(10), collecting_number character varying(255), collecting_institute character varying(255), collecting_institute_code character varying(6), breeder_institute character varying(255), breeder_institute_code character varying(6), breeding_country character varying(255), breeding_country_code character varying(3), breeding_system character varying(255), pedigree character varying(255), cultivar character varying(255), full_scientific_name character varying(255), genus character varying(255), species character varying(255), taxon_author character varying(255), vernacular_name character varying(255), uddi_id integer, data_provider character varying(255), creusr character varying(32) DEFAULT current_user, credtm timestamp(0) without time zone DEFAULT now(), updusr character varying(32) DEFAULT current_user, upddtm timestamp(0) without time zone DEFAULT now() )
This is the harvested germplasm sample (accession level) data harvested from the BioCASE entry points

institute

CREATE TABLE institute ( institute_id serial NOT NULL, institute_name character varying(255), institute_acronym character varying(50), institute_address character varying(255), institute_address_zip character varying(255), institute_address_country character varying(255), institute_url character varying(255), institute_email character varying(255), instcode character varying(7), institute_remarks text, image_logo character varying(255), image_illustration character varying(255), credtm timestamp(0) without time zone DEFAULT now(), creusr character varying(32), upddtm timestamp(0) without time zone DEFAULT now(), updusr character varying(32) )
Index of institutes providing data or otherwise described within the CHM.

person

CREATE TABLE person ( person_id serial NOT NULL, person_name character varying(120), person_email character varying(100), person_email_2 character varying(100), person_title character varying(40), first_name character varying(80), last_name character varying(80), username character varying(32), password character varying(32), institute_id integer, institute_id_2 integer, image_person character varying(255), person_remarks text, credtm timestamp(0) without time zone DEFAULT now(), creusr character varying(32) DEFAULT CURRENT_USER, updusr character varying(32) DEFAULT CURRENT_USER, upddtm timestamp(0) without time zone DEFAULT now() )
Index of persons providing data or otherwise described within the CHM.

page

CREATE TABLE page ( page_id serial NOT NULL, page_title character varying(60), page_description character varying(200), remarks text, creusr character varying(32) DEFAULT CURRENT_USER, credtm timestamp(0) without time zone DEFAULT now(), updusr character varying(32) DEFAULT CURRENT_USER, upddtm timestamp(0) without time zone DEFAULT now() )
CHM information web pages (NOT IN USE, YET!)

visit_log

CREATE TABLE visit_log ( visit_id serial NOT NULL, username character varying(32), session_id character varying(100), entry_dtm timestamp(0) without time zone, visit_duration character varying(80), remote_addr text, http_accept_language text, http_user_agent text, scope character varying, script_uri character varying(300), request_uri character varying(300), remote_addr_ns_lookup character varying(300), person character varying(300), institute character varying(300), browser character varying(200), credtm timestamp(0) without time zone DEFAULT now(), creusr character varying(32) DEFAULT current_user, upddtm timestamp(0) without time zone DEFAULT now(), updusr character varying(32) DEFAULT current_user )
Logging the visitors to the site.

visit_event

CREATE TABLE visit_event ( visit_event_id serial NOT NULL, event character varying(100), person character varying(200), institute character varying(200), visit_id integer, username character varying(32), request_uri character varying(300), session_id character varying(300), scope character varying(10), visit_duration character varying(100), script_uri character varying(100), remarks text, error boolean DEFAULT false, creusr character varying(32) DEFAULT current_user, credtm timestamp(0) without time zone DEFAULT now(), updusr character varying(32) DEFAULT current_user, upddtm timestamp(0) without time zone DEFAULT now() )
Logging the visitors to the site.

mcpd

CREATE TABLE mcpd ( mcpd_id serial NOT NULL, instcode character varying(6), accenumb character varying(100), collnumb character varying(100), collcode character varying(6), genus character varying(100), species character varying(100), spauthor character varying(100), subtaxa character varying(100), subtauthor character varying(100), cropname character varying(100), accename character varying(100), acqdate character varying(8), origcty character varying(3), collsite character varying(200), latitude character varying(7), longitude character varying(8), elevation integer, colldate character varying(8), bredcode character varying(6), sampstat character varying(3), ancest character varying(200), collsrc character varying(2), donorcode character varying(6), donornumb character varying(100), othernumb character varying(200), duplsite character varying(6), storage character varying(2), remarks text )
Multi Crop Passport - Dataset (NOT IN USE)

dataset

CREATE TABLE dataset ( dataset_id serial NOT NULL, publisher_institute character varying(100), publisher_institute_code character varying(6), contact_name character varying(100), contact_email character varying(100), source_last_update timestamp(0) without time zone )
This is the harvested dataset. Metadata collected from /DataSets/DataSet (NOT IN USE!)

address

CREATE TABLE address ( address_id serial NOT NULL, street_address character varying(255), box_address character varying(255), zip_code character varying(255), zip_name character varying(255), country character varying(255), remarks text, credtm timestamp(0) without time zone DEFAULT now(), creusr character varying(32) DEFAULT CURRENT_USER, updusr character varying(32) DEFAULT CURRENT_USER, upddtm timestamp(0) without time zone DEFAULT now() )
Index of address for contacts (NOT IN USE!).
Genetic Diversity
  • Why is biodiversity important?
  • What is genetic diversity?
  • Why conserve germplasm?
  • Germplasm Databases
  • Global germplasm index
  • Germplasm Clearing House Mechanism (about)
Information and links
  • Genetic resources, EC ABS portal, EC Biotechnology
  • Geo-referenced germplasm data and maps
CHM Sections (under development)
  • Data Providers (BioCASE)
  • Data Standards (Schema)
  • Data HARVEST
  • Data IMPORT
  • Germplasm Data
  • Contact institutes, persons
  • CHM Data Model
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