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Mapping the Multi-Crop Passport Descriptors (MCPD) onto ICIS

The multi-crop passport descriptors are an agreed international standard, in flat file format (one row per accession, one column per field) for sharing passport data that are common to all crops.

These passport data are stored in several different tables in the GMS of ICIS. This page maps the MCPD onto to the corresponding fields in ICIS.

The accession, the donor's sample, and the collected or bred sample

A major structural difference between MCPD and ICIS is the handling of donor's sample, the collected sample and the bred sample.

• In MCPD, one record corresponds to one accession, and information about the donor's sample, collected sample and bred sample is recorded as different fields of that record.
• In ICIS, up to three GIDs are used for each accession:

1. GID for the accession itself;
2. GID for the sample held by the donor, pointed to by GPID2 of the accession GID; and
3. GID for the original cross or collected sample, pointed to by GPID1 of the accession GID.

To retrieve them in IRIS, 3 instances of the GERMPLSM, NAMES, ATRIBUTS and LOCATION tables are needed, joined by GPID1 and GPID2. In this page, the three instances are referred to as:

• g, n, a, L = instance of germplasm, names, atributs or location tables used for the accession itself, joined by g.GID=n.GID etc
• g1, n1, a1, L1 = instance of germplasm, names, atributs or location tables used for the original cross or collected sample, joined by g.GPID1=g1.GID and g1.GID=n1.GID etc
• g2, n2, a2, L2 = instance of germplasm, names, atributs or location tables used for the donor's sample, joined by g.GPID2=g2.GID and g2.GID=n2.GID etc

The Map

 

MCPD field	Brief description	Equivalent in IRIS
01. InstCode	FAO Code of the institute maintaining the sample	institut.faocode where institut.locid=g.glocn
02. AcceNumb	"Accession number" as the sample's unique ID.	n.nval where n.nstat=8 (i.e. the name is a preferred ID) For data strictly on genebank accessions, also restrict to names.ntype=1 (i.e. the name is the ID of a genebank accession); however this restriction may be relaxed if other types of material are to be included, e.g. breeding lines or entries in international nurseries. Also if we are including non-genebank accessions there may be GIDs that do not have a name with nstat=8. In this case, we use the "ICIS unique ID", which in the case of rice = "IRIS" & g.germuid & g.lgid
03. CollNumb	Collecting number = sample ID assigned by collector when collected	(Only for a GID derived by derivative or maintenance methods from an original collected sample, i.e. where g1.methn=69) n1.nval where n1.nstat=8 and n1.ntype=9 and g1.methn=69
04. CollCode	Collecting institute code	(Only for a GID derived by derivative or maintenance methods from an original collected sample, i.e. where g1.methn=69) institute.faocode where g1.gid=listdata.gid and listdata.listid=listnms.listid and teammember.listid=listdata.listid and listnms.listtype=collmiss and teammember.personid=persons.personid and institute.institid=person.personid
05. Genus 06. Species 07. SpAuthor 08. Subtaxa 09. SubtAuth	ICIS doesn't (yet) handle taxonomy as separate fields. Instead these fields are merged into a single string as an attribute	If (a.gid=g.GID and a.AID=1141) is not null (i.e. if the accession has an attribute 1141), scaledis.valdesc where scaledis.scaleid=532 and a.aval=scaledis.value and a.gid=g.GID and a.AID=1141 If the GID has no attribute with AID=1141, it may be possible to put a default for the database. For IRIS, we assume "Oryza sativa (L.)" for missing attribute 1141.
10. CropName	Common crop name	If (a.gid=g.GID and a.AID=1133) is not null (i.e. if the accession has an attribute 1133), scaledis.valdesc  where scaledis.scaleid=526 and a.aval=scaledis.value and a.gid=g.GID and a.AID=1133 If the GID has no attribute with AID=1133, it may be possible to put a default for the database. For IRIS, this is "rice" Append n.nval where n.ntype=23
11. AcceName	Accession name	Start with the preferred name (n.nval where n.nstat=1). If there are non-preferred names that are not included elsewhere in the MCPD (i.e. n.nstat=0 and n.ntype= one of [4,5,6,7,10,11,12,13,15,16,17,20,24] ), concatenate them, separating successive names with ";".
12. AcqDate	Acquisition date	g.GDATE
13. OrigCty	Country of origin	L1C.lname where L1C.locid=L1.cntryID and L1.locid=g1.glocn (where L1C and L1 are two separate instances of the LOCATION table)
14. CollSite	Location of collecting site	(Only for a GID derived by derivative or maintenance methods from an original collected sample, i.e. where g1.methn=69): Concatenation of L1.lname, L1T.lname, L1D.lname, L1P.lname where L1.locid=g1.glocn and L1.snl3id=L1T.locid and L1.snl2id=L1D.locid and L1.snl1id=L1P.locid (where L1P, L1D, L1T and L1 are four separate instances of the location table, documenting respectively the province, district, town and location)
15. Latitude	Latitude of collecting site	(Only for a GID derived by derivative or maintenance methods from an original collected sample, i.e. where g1.methn=69) georef.lat where georef.locid=g1.locn and g1.methn=69
16. Longitud	Longitude of collecting site	(Only for a GID derived by derivative or maintenance methods from an original collected sample, i.e. where g1.methn=69) georef.lon where georef.locid=g1.locn and g1.methn=69
17. Elevatio	Altitude of collecting site	(Only for a GID derived by derivative or maintenance methods from an original collected sample, i.e. where g1.methn=69) georef.alt where georef.locid=g1.locn and g1.methn=69
18. CollDate	Collecting date of sample	(Only for a GID derived by derivative or maintenance methods from an original collected sample, i.e. where g1.methn=69) g1.gdate where g1.methn=69
19. BredCode	Breeding institute code	(Only for a GID derived by derivative or maintenance methods from a cross, i.e. where g1.methn has a GEN type) institut.faocode where institut.locid=g1.glocn
20. SampStat	Biological status of accession	If (a.gid=g.GID and a.AID=1144) is not null (i.e. if the accession has an attribute 1144), scaledis.valdesc where scaledis.scaleid=532 and a.aval=scaledis.value Otherwise, if (n.ntype=4) is not null or (n.ntype=20) is not null, put "Improved cultivar" Otherwise, if methods.mtype="DER" where methods.mid=g.methn, put "Breeding line" Otherwise null
21. Ancest	Pedigree	(Only for a GID derived by derivative or maintenance methods from a cross, i.e. where g1.methn has a GEN type) Constructed dynamically from the pedigree in ICIS
22. CollSrc	Collecting/acquisition source	(Only for a GID derived by derivative or maintenance methods from an original collected sample, i.e. where g1.methn=69) scaledis.valdesc where scaledis.scaleid=527 and a.aval=scaledis.value and a.gid=g.GID and a.AID=1135
23. DonorCode	Donor institute code	institut.faocode where institut.locid=g2.glocn
24. DonorNum	Donor accession number	n2.nval where n2.nstat=8
26. DuplSite	Location of safety duplicates	(This is information in IRIS-GRIMS is present only in the local database, not publicised in central)
27. Storage	Type of germplasm storage	(This is information in IRIS-GRIMS is present only in the local database, not publicised in central)
28. Remarks	Remarks	"NOTES" attribute: a.aval where a.AID=103 and a.gid=g.gid