215 lines
15 KiB
Plaintext
215 lines
15 KiB
Plaintext
head 1.9;
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access;
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symbols;
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locks; strict;
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comment @# @;
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1.9
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date 2006.01.24.18.40.14; author DagTerje; state Exp;
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branches;
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next 1.8;
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1.8
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date 2006.01.20.11.57.44; author DagTerje; state Exp;
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branches;
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next 1.7;
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1.7
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date 2006.01.20.11.57.18; author DagTerje; state Exp;
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branches;
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next 1.6;
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1.6
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date 2006.01.20.11.31.05; author DagTerje; state Exp;
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next 1.5;
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1.5
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date 2005.11.14.00.40.06; author DagTerje; state Exp;
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next 1.4;
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1.4
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date 2005.11.14.00.36.58; author DagTerje; state Exp;
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date 2005.11.14.00.14.24; author DagTerje; state Exp;
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next 1.2;
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1.2
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date 2005.11.12.23.08.48; author DagTerje; state Exp;
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next 1.1;
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1.1
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date 2005.11.12.22.39.26; author DagTerje; state Exp;
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next ;
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1.9
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log
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@minor change category navigation page foot
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@---+++++ Germplasm accession identificators
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The plant germplasm can be conserved as seed samples, clones maintained _in situ_ or _in vivo_, cry-preseved etc. by genebank institutes world wide. Most germplasm samples are from the economicaly valuable food crops. Also the crop wild relatives are preserved. And some collects of wild plant material are sometimes preserved as a safe backup for biodiversity. Domesticated animals (husbandry) are also part of the germplasm, stored by genebanks. The germplasm collections are living collections. The conserved material need to be regenerated when the material loose vitality. The vitaly of the germplasm samples are regularly monitored (every 5-10 year). The regeneration cycle varies from species to species and between select conservation forms. A normal regeneration cycle for seed samples of the most common crops is around 20 to 50 years. The most common data exchange format for plant germplasm data is the [[http://www.ipgri.cgiar.org/publications/pdf/124.pdf][MCPD]] (Multi Crop Passport Descriptors).
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---+++++ The composite 'GUID' for Germplasm accessions
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The global identifiers are an importent item on the agenda of the plant genetic resources (PGR) community. The three concepts *genus*, *genebank* (holding institute) and *accession number* (unit ID) mostly provide an acceptable unique key to the germplasm accessions. But the ongoing move to more machine data discovery and interoperability issues through web services, the LSIDs becomes a very useful element.
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* *Genus* - The cultivated plants belong to a very limited number of taxons. The genus name used to describe the germplasm samples are mostly not controversial and provides a stable part of the composite key used to uniquely identify germplasm accessions. (It does however happen that an accession is not identified correctly. For NGB in particular the grasses have proven difficult ot get correctly identified. Sometimes even the Genus name needs to be corrected!)
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* *Holding institute* - The genebanks, or institutes holding the physical germplasm sample, are assigned a unique number, institute code, in the [[http://apps3.fao.org][FAO WIEWS database]]. This number is used as part of the composite unique key. The institute code or the holding institute may however in unusual cases be changed. If the germplasm collection is divided in two new genebanks. For example when a country or federation is divided in two or more new countries, Yugoslavia, Soviet, Czechoslovakia... Germplasm collections can also be combined or transfered to another genebank. One example is the reorganisation of the genebanks of the former East and West Germany where seed samples was transfered from the previous conservation in West to the Eastern genebank. In most cases the institute code to design the holding institute is stable.
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* *Accession number* (Specimen ID) - The germplasm samples are assigned a unique number within the sub-collection. Most genebanks assign accession numbers unique within the entire institute. The accession numbers are often given as integer numbers or as a character followed by an integer number (34, 00034, PI56, H9879, K6787, K-5676 etc). The accession number prefixes are not standardized and more than one institute can often use the same prefix. This complicates the interoperability of accession level metadata from different sources. Often the accession number is composed as the intitute acronym together with a serial number. Example from the Nordic Gene Bank (NGB), NGB12, NGB10776... Other genebanks assign accession numbers that are only unique within a sub-collection. The sub-collections are often divided by crop (potato, barley, wheat, maize...). Different sub-collections mostly do not share samples from the same genus.
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---+++++ Other Germplasm identificators
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The Germplasm accessions (specimen) are classified by several other accession identificators.
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* *Accession name* - Most germplasm accessions are given both an _accession number_ and an _accession name_. The accession name is often the cultivar name used by the breeder, the landrace name or the breeding line number.
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* *Collecting number* (collectors sample number) - The accession code assigned by the person collecting the germplasm sample is the most original accession identificator and of large value when searching duplicates between the world wide genebank germplasm collections. Conserved germplasm material from outside the country of the plant breeder or scientist was often ordered via the relevant national genebank. The national genebank often kept a part of the received (plant seed) material to be part of the local germplasm collection.
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* *Breeders accession designation* (breeding line) - Most samples of the genebanks are in fact not collected in the wild, but rather the result of a breeding program where the desired properties of the crop is carefully selected for. The breeding line number and other designations assigned to the plant material in this process is the most original accession identificator of this type of material. For these accessions the pedigree of the material crossed to obtain the new accession is carefully recorded and registered by the genebank.
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* *Commercial cultivar name* - the germplasm produced by breeding are classified by the cultivar name given by the breeding company in marketing and sale of the seeds. Several conserved accessions can be classified as belonging to the same cultivar.
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* *Landrace name* - Further other accessions belong to a landrace. A landrace is traditional material developed by local farmers. The landrace does not have a given known breeder.
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* *Donor accession designation* - The germplasm accessions are distributed between genebanks and a _duplicate_ often becomes part of the second collection. This _duplicate_ can then be distributed further and become part of a third genebank collection ... and so on. Each genebank adding the sample to their local collection assigns a new local accession number and record the previous accession number used by the genebank donating the sample as the donor designation. Some genebanks try to register as far as possible the full chain of donor events and can have several *donor accession designations* for one local accession.
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* *_Other_ accession designations* - The international data exchange format for germplasm accessions is the Multi Crop Passport Descriptor List (MCPDL) developed by IPGRI, Rome. This descriptor list has a concept *OTHERNUMB* for unspecified additional identification numbers. Many genebanks (including NGB) have a concept in their local database to register these _other accession numbers_. Most often the numbers here are earlier donors designations prior to the institute or person donating the accession to the local genebank in question.
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---+++++ Germplasm origin - collecting and breeding events
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The identificator numbers can perhaps be better understood classified to two events where new germplasm is defined or created. There are two original sources of new accessions for the germplasm genebanks. The *Collecting/Gathering* event and the *Breeding/Cultivation* event.
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---+++++ Donation events
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Germplasm accessions can be donated to a genebank from a collector, a breeder or from other sources. Germplasm accessions are also often 'donated' from one genebank to another genebank and germplasm from the very same origin (gathering event or breeding event) get 'duplicated' accross the genebank collections. This is not neccessary negative as the germplasm sample duplication can be concidered a safe copy. from a national point of view the national genebank has the mandate of conserving germplasm of value to the country. But from a global management perspective it is often difficult to estimate the number of unique germplasm accessions worldwide. A global index of the original gathering and breeding events as well as GUID technology to describe the relationship between metadata classes would be of great value to achieve more efficient global management of global germplasm collections.
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----
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Category [[GUIDUseCases][GUID Use Cases]], [[GUIDsForCollectionsAndSpecimens][Donalds questions]], response to the questions [[IdentifiersForGermplasm][for germplasm identifiers]]@
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1.8
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@d37 2
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a38 1
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Back to [[GUIDUseCases][GUID Use Cases]]@
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1.7
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a3 1
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The plant germplasm can be conserved as seed samples, clones maintained _in situ_ or _in vivo_, cry-preseved etc. by genebank institutes world wide. Most germplasm samples are from the economicaly valuable food crops. Also the crop wild relatives are preserved. And some collects of wild plant material are sometimes preserved as a safe backup for biodiversity. Domesticated animals (husbandry) are also part of the germplasm, stored by genebanks. The germplasm collections are living collections. The conserved material need to be regenerated when the material loose vitality. The vitaly of the germplasm samples are regularly monitored (every 5-10 year). The regeneration cycle varies from species to species and between select conservation forms. A normal regeneration cycle for seed samples of the most common crops is around 20 to 50 years. The most common data exchange format for germplasm data is the [[http://www.ipgri.cgiar.org/publications/pdf/124.pdf][MCPD]] (Multi Crop Passport Descriptors).
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@d3 1
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a3 1
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The plant germplasm can be conserved as seed samples, clones maintained _in situ_ or _in vivo_, cry-preseved etc. by genebank institutes world wide. Most germplasm samples are from the economicaly valuable food crops. Also the crop wild relatives are preserved. And some collects of wild plant material are sometimes preserved as a safe backup for biodiversity. Domesticated animals (husbandry) are also part of the germplasm, stored by genebanks. The germplasm collections are living collections. The conserved material need to be regenerated when the material loose vitality. The vitaly of the germplasm samples are regularly monitored (every 5-10 year). The regeneration cycle varies from species to species and between select conservation forms. A normal regeneration cycle for seed samples of the most common crops is around 20 to 50 years.
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1.5
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@added back to GUID Use Cases link
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@d10 3
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a12 1
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* *Accession number* (Specimen ID) - The germplasm samples are assigned a unique number within the sub-collection. Most genebanks assign accession numbers unique within the entire institute. The accession numbers are often composed as the intitute acronym together with a running number. Example from the Nordic Gene Bank (NGB), NGB12, NGB10776... Other genebanks assign accession numbers that are only unique within a sub-collection. The sub-collections are often divided by crop (potato, barley, wheat, maize...). Different sub-collections mostly do not share samples from the same genus.
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d18 1
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a18 1
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* *Accession name* - Most germplasm accessions are given both a _number_ and a _number_. The accession name is often the cultivar name used by the breeder, the landrace name or the breeding line number.
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d27 4
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a30 1
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---+++++ Collecting, breeding and donation events
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d32 2
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a33 1
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The identificator numbers can perhaps be better understood classified to three events where new IDs are defined. There are three sources of new accessions for the germplasm genebanks. The *Collecting/Gathering* event, the *Breeding* event and the *Donation* event. Accessions can be donated to a genebank from a collector, a breeder or from other sources.
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@
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1.4
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@minor formatting
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@
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@d27 5
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a31 1
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The identificator numbers can perhaps be better understood classified to three events where new IDs are defined. There are three sources of new accessions for the germplasm genebanks. The *Collecting/Gathering* event, the *Breeding* event and the *Donation* event. Accessions can be donated to a genebank from a collector, a breeder or from other sources.@
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1.3
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@Added accession name and the *other* accession number.
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@d22 1
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a22 1
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* *_Other_ accession designations* - The international data exchange format for germplasm accessions is the Multi Crop Passport Descriptor List (MCPDL) developed by IPGRI, Rome. This descriptor list have a concept *OTHERNUMB* for additional identificator numbers described above. Many genebanks (including NGB) have a concept in the local database to register these _other accession number_. Most often the numbers here are donors numbers prior to the institute or person donating the accession to the local genebank in question.
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@
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1.2
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@minor formatting
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@d8 1
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a8 1
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* *Genus* - The cultivated plants belong to a very limited number of taxons. The genus name used to describe the germplasm samples are mostly not controversial and provides a stable part of the composite key used to uniquely identify germplasm accessions.
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d12 1
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d16 1
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d18 1
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a18 1
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* *Breeders accession designation* - Most samples of the genebanks are in fact not collected in the wild, but rather the result of a breeding program where the desired properties of the crop is carefully selected for. The breeding line number and other designations assigned to the plant material in this process is the most original accession identificator of this type of material. For these accessions the pedigree of the material crossed to obtain the new accession is carefully recorded and registered by the genebank.
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d22 2
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d25 1
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d27 1
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a27 1
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{{color c="blue" text="In-progress, I will add some more identificators..."}}@
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1.1
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@Initial revision
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@d3 1
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a3 1
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The plant germplasm can be conserved as seed samples, clones maintained in situ or in vivo, cry-preseved etc. by genebank institutes world wide. Most germplasm samples are from the economicaly valuable food crops. Also the crop wild relatives are preserved. And some collects of wild plant material are sometimes preserved as a safe backup for biodiversity. Domesticated animals (husbandry) are also part of the germplasm, stored by genebanks. The germplasm collections are living collections. The conserved material need to be regenerated when the material loose vitality. The vitaly of the germplasm samples are regularly monitored (every 5-10 year). The regeneration cycle varies from species to species and between select conservation forms. A normal regeneration cycle for seed samples of the most common crops is around 20 to 50 years.
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@
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