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License: Apache License 2.0
Genomic Biodiversity Interest Group
License: Apache License 2.0
I recommend using a TDWG mailing list, but we could also create a Google group, if people prefer.
I am no currently able to access https://lists.tdwg.org/mailman/listinfo, but I will try again later or @timrobertson100 to do it.
Field | Value |
---|---|
subject_id | http://data.ggbn.org/schemas/ggbn/terms/preparationMaterials |
subject_definition | Materials and chemicals used in the preparation of the specimen, tissue, DNA or RNA sample |
subject_usage_notes | |
subject_examples | for DNA: DNeasy blood and tissue kit, CTAB; |
predicate_id | skos:narrowMatch |
object_id | MIXS:0000037 |
object_label | nucl_acid_ext |
object definition | A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
and
Field | Value |
---|---|
subject_id | http://data.ggbn.org/schemas/ggbn/terms/purificationMethod |
subject_definition | Method or protocol used for secundary purification of already extracted genomic DNA or of PCR product |
subject_usage_notes | no controlled vocabulary; this element should be used both for DNA and Amplification product; repeatable only within GGBN Amplification Vocabulary |
subject_examples | QIAamp DNA Mini Kit |
predicate_id | skos:narrowMatch |
object_id | MIXS:0000037 |
object_label | nucl_acid_ext |
object definition | A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
Following on from #4 - I don't seem to be able to create GH Projects. Is this a permissions issue (I don't seem to have admin rights here, which would be needed for me and @raissameyer) or should we use Labels to mark TG-specific issues instead?
Dear GBWG team @ramonawalls
@raissameyer and I have created a task group proposal to consolidate this multi-year thread here.
This issue is to notify the GBWG community and respond to questions. It's also a chance to consolidate issues like #3
Field | Value |
---|---|
subject_id | http://rs.tdwg.org/dwc/terms/higherGeography |
subject_definition | A list (concatenated and separated) of geographic names less specific than the information captured in the locality term. |
subject_usage_notes | Recommended best practice is to separate the values in a list with space vertical bar space ( | ), with terms in order from least specific to most specific. |
subject_examples | North Atlantic Ocean , "South America | Argentina | Patagonia | Parque Nacional Nahuel Huapi | Neuquén | Los Lagos" (with accompanying values South America in continent, Argentina in country, Neuquén in stateProvince, and Los Lagos in county. |
predicate_id | skos:exactMatch |
object_id | MIXS:0000010 |
object_label | geo_loc_name |
object definition | The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
comment | DwC term encompasses any combination of geographic region names, while the MIxS term may either be the name of a country or a sea, followed by additional region information. |
Field | Value |
---|---|
Term | Bulk Sample |
Definition | tbd |
Examples | tbd |
Reference | tbd |
DwC:materialSample | tbd |
ABCD:KindOfUnit | tbd |
GGBN:materialSampleType | tbd |
Comment | GGBN developed a preparation vocabulary including date, person, method, materials and type of preparation, hence the new more precise term "preparationType" |
Field | Value |
---|---|
Term | Environmental Sample |
Definition | A material sample dedicated to multiple taxa that (i) represents taxonomic biodiversity from across the tree of life (e.g. blood, gut), (ii) represents abiotic substrate or environment (e.g. soil, water, ice core) or (iii) an assemblage of both |
Examples | blood, gut, soil, water, sediment |
Reference | Droege,G. et al. (2016), https://doi.org/10.1093/database/baw125 |
DwC:materialSample | Environmental Sample |
ABCD:KindOfUnit | Environmental Sample |
GGBN:materialSampleType | Environmental Sample |
Comment | Examples in DwC are more equal to what in terms of GGBN is preparationType; the GGBN term "materialSampleType" has been developed to work with DwC as ABCD already has an appropriate term so not needed there but "KindOfUnit" is not used by DwC; GGBN developed a preparation vocabulary including date, person, method, materials and type of preparation, hence the more precise term "preparationType"; |
Field | Value |
---|---|
subject_id | http://data.ggbn.org/schemas/ggbn/terms/sequencingMethod |
subject_definition | Method or protocol used to generate the DNA or RAD sequences/reads |
subject_usage_notes | currently to be used with ABCD only |
subject_examples | Genotyping-by-sequencing (GBS) |
predicate_id | skos:exactMatch |
object_id | MIXS:0000050 |
object_label | seq_meth |
object definition | Sequencing method used; e.g. Sanger, pyrosequencing, ABI-solid |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
Field | Value |
---|---|
Term | Community (bulk) DNA |
Definition | DNA from bulk samples (e.g. plankton samples or Malaise trap samples consisting of several individuals from many species) |
Examples | tbd |
Reference | GBIF guide, https://doi.org/10.35035/doc-vf1a-nr22 |
DwC:materialSample | DNA |
ABCD:KindOfUnit | DNA |
GGBN:materialSampleType | DNA |
DwC:preparations | tbd |
ABCD:preparationType | ABCD uses GGBN term |
GGBN:preparationType | tbd |
Comment | Different communities seem to use this term in various contextes (i) e.g. an insect trap with one ore more taxa, (ii) a pooled sample from different organisms, but same taxon; There seem to be different methods used for eDNA and bulk DNA analysis |
or
Field | Value |
---|---|
Term | Community DNA |
Definition | Refers to DNA extracted from a mixture of different organisms. Could be eDNA (environmental samples almost always contain DNA from a mixture of species) or organismal DNA (e.g. homogenised insect trap samples) |
Examples | tbd |
Reference | https://www.naturemetrics.co.uk/info-hub/edna-glossary/ |
Field | Value |
---|---|
subject_id | http://data.ggbn.org/schemas/ggbn/terms/marker |
subject_definition | Genetic locus/marker or DNA fragment amplified by PCR |
subject_usage_notes | |
subject_examples | COI, rbcL |
predicate_id | skos:exactMatch |
object_id | MIXS:0000044 |
object_label | target_gene |
object definition | Targeted gene or locus name for marker gene studies |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
The IG should come up with definitions for environmental sample, environmental DNA (in comparison to single species samples), abiotic versus biotic environments etc.
Examples from Droege et al. 2016 doi: 10.1093/database/baw125:
Examples from GBIF Publishing DNA derived data glossary (https://docs.gbif-uat.org/publishing-dna-derived-data/1.0/en/#glossary):
Hi @wdduncan
The MIxS IRIs are going to be essential for this Task Group. Great that you are developing them!
Would you know if there is a Beta release just for us to experiment with? If so, would you mind linking to that resource here?
Best,
Raïssa
This came up in the GSC. See GenomicsStandardsConsortium/mixs#90. MIxS does not have terms to say who carried out various roles in a project, and DwC only has a few roles, like who did the identification or took a measurement. Does GGBN have terms like this?
@79-6d
Field | Value |
---|---|
subject_id | http://rs.tdwg.org/dwc/terms/associatedOrganisms |
subject_definition | A list (concatenated and separated) of identifiers of other Organisms and their associations to this Organism. |
subject_usage_notes | |
subject_examples | "sibling of":"DMNS:Mamm http://arctos.database.museum/guid/DMNS:Mamm:14171" , "parent of":"MSB:Mamm http://arctos.database.museum/guid/MSB:Mamm:196208" | "parent of":"MSB:Mamm http://arctos.database.museum/guid/MSB:Mamm:196523" | "sibling of":"MSB:Mamm http://arctos.database.museum/guid/MSB:Mamm:142638" |
predicate_id | skos:exactMatch |
object_id | MIXS:0000028 |
object_label | biotic_relationship |
object definition | Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
comment | One could also capture relationships with more metadata about the assertion using the ResourceRelationship extension to Darwin Core. |
Field | Value |
---|---|
subject_id | http://rs.tdwg.org/dwc/terms/eventDate |
subject_definition | The date-time or interval during which an Event occurred. For occurrences, this is the date-time when the event was recorded. Not suitable for a time in a geological context. |
subject_usage_notes | Recommended best practice is to use a date that conforms to ISO 8601-1:2019. |
subject_examples | 1963-03-08T14:07-0600 (8 Mar 1963 at 2:07pm in the time zone six hours earlier than UTC). 2009-02-20T08:40Z (20 February 2009 8:40am UTC). 2018-08-29T15:19 (3:19pm local time on 29 August 2018). 1809-02-12 (some time during 12 February 1809). 1906-06 (some time in June 1906). 1971 (some time in the year 1971). 2007-03-01T13:00:00Z/2008-05-11T15:30:00Z (some time during the interval between 1 March 2007 1pm UTC and 11 May 2008 3:30pm UTC). 1900/1909 (some time during the interval between the beginning of the year 1900 and the end of the year 1909). 2007-11-13/15 (some time in the interval between 13 November 2007 and 15 November 2007). |
predicate_id | skos:narrowMatch |
object_id | MIXS:0000011 |
object_label | collection_date |
object definition | The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
comment |
Field | Value |
---|---|
subject_id | http://data.ggbn.org/schemas/ggbn/terms/markerSubfragment |
subject_definition | Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes |
subject_usage_notes | |
subject_examples | V6 |
predicate_id | skos:exactMatch |
object_id | MIXS:0000045 |
object_label | target_subfragment |
object definition | Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
Hey,
So relationship between samples was brought up in MIxS meeting yesterday. It makes me wonder what is the best way to represent biological replicates and technical replicates of sequence based data in DwC?
As recommended in the guidelines to publish DNA-derived data through biodiversity data platforms:
We do, however, recommend including an eventID for each core record, to indicate the association between occurrences derived from the same sampling event.
Can I understand that this can be used to address technical replicates since technical replicates are sub-samples of a sample? What about biological replicates? and what do you think about the use of resource relationship extension?
@timrobertson100 Do you think that perhaps this is interesting to be included in the the guidelines to publish DNA-derived data through biodiversity data platforms?
I just gonna dump some other information that I can find here:
Please see this google doc for more info.
If I understand correctly, the attributes as mentioned in ENA and INSDC samples are not part of MIxS? (can someone please correct me if I am wrong? thank you) But I think this information is important and should be represented in DwC imho.
Parent child relationships are established via ‘sample composed of’ and ‘sample derived from’ attributes.
These attributes are captured within the child sample and their value is a list of INSDC sample IDs (comma separated) or a range (no spaces) e.g.:
sample derived from: ERS123456,ERS123654,ERS123123
sample composed of: SAME1234567-SAME1235000
Example use: https://www.ebi.ac.uk/ena/browser/view/SAMEA6150246 (click additional attributes)
uses resource relationships from DwC
NCBI uses the same relationship attributes that are present in EBI BioSample:
(you can view BioSample attribute definitions here: https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/)
same as
indicates that the same physical sample has multiple BioSample records
https://www.ncbi.nlm.nih.gov/biosample/?term=SAMEA4447240
derived from
indicates where one BioSample was derived from another BioSample
https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN13192999
family role
relationships to other samples in the same study; can include multiple relationships
https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN01090941
child of
indicates parentage; only applicable to sexual organisms, for bacteria use 'derived from'
https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN00690380
microbiomedata/nmdc-metadata#287
GenomicsStandardsConsortium/mixs#36
Thank you so much!
Field | Value |
---|---|
subject_id | http://purl.org/dc/terms/references |
subject_definition | A related resource that is referenced, cited, or otherwise pointed to by the described resource. |
subject_usage_notes | |
subject_examples | http://arctos.database.museum/guid/MVZ:Mamm:165861 , http://www.catalogueoflife.org/annual-checklist/show_species_details.php?record_id=6197868 |
predicate_id | skos:closeMatch |
object_id | MIXS:0000091 |
object_label | url |
object definition | |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
comment | This mapping is a guess, given that the MIxS url term does not have a definition provided. |
Recommendation from guidelines to publish DNA-derived data through biodiversity data platforms
The current recommendation is to publish data as Occurrence core (Category I or II) with the DNA derived data extension. This approach compensates for limitations of the DwC star schema, which would not allow any occurrence-level data in extension files (such as processed barcode sequences) to point to records in an event core file. We do, however, recommend including an eventID for each core record, to indicate the association between occurrences derived from the same sampling event
Concern raised during meeting on 2021-02-09
using the extended Measurements of Fact extension, if another extension is added they can only use the occurrence core, no longer the event core.
Challenge because a lot of the observations include environmental data, image based data and aggregating everything into events is what their community wants.
Similarly I also think that many environmental measurements such as depth
related terms will have to be replicated many times for each occurrence record.
The specification/definition of terms may impact structure of the data model implementations.
For example, in a relational model, many-to-many relations between tables often result in complex schemas and/or result in ad-hoc work arounds. They also may create issue for denormalized schemas, such as star schemas.
Some examples from the healthcare domain:
one patient can be under the care of many physicians; one physician can care for many patients
one tooth surface can contain many fillings; one filling can cover many tooth surfaces
one anatomical site can contain many cancers; one cancer can be located in multiple anatomical sites
In each of the examples above, the definitions for patient, physician, tooth surface, anatomical site, cancer may be agnostic with respect to the arity of relation between the entities. However, issues arise when creating a data model to capture this information, or even when preparing spreadsheets for submission.
e.g. https://to.be.decided/MIXS:0000056
Field | Value |
---|---|
Term | Genomic Sample |
Definition | Any biological material preserved to keep its molecular properties. Subset of "Material Sample". |
Examples | specimen, culture, DNA, RNA, tissue, environmental sample (or eSample) |
Reference | Droege,G. et al. (2016), https://doi.org/10.1093/database/baw125 |
DwC:basisOfRecord | MaterialSample |
ABCD:RecordBasis | MaterialSample |
comment | In its data standard terms GGBN does not flag "contains molecular properties" yet. A s a community convention only biological material that contains molecular properties should be shared through the GGBN Data Portal (hence its name...). Outside of GGBN this machine readable information might be important though, e.g. certain types of blood samples don't contain DNA. |
Field | Value |
---|---|
Term | Ancient Genomic DNA |
Definition | The physical result of DNA extraction of a tissue sample older than 100 years (e.g. bones) containing DNA from a single taxon. Usually not completely consumed during sequencing and deposited in a biodiversity biobank |
Examples | aDNA |
Reference | Droege,G. et al. (2016), https://doi.org/10.1093/database/baw125 |
DwC:materialSample | DNA |
ABCD:KindOfUnit | DNA |
GGBN:materialSampleType | DNA |
DwC:preparations | tbd |
ABCD:preparationType | ABCD uses GGBN term |
GGBN:preparationType | aDNA |
Comments | GGBN developed a preparation vocabulary including date, person, method, materials and type of preparation, hence the new more precise term "preparationType" |
Create a spreadsheet in which each package only contains terms for the package; i.e., remove the core terms from the packages.
Field | Value |
---|---|
Term | Tissue Sample |
Definition | A material sample dedicated to a single taxon (e.g. leaf, muscle, leg), often chemically or physically treated to preserve biomolecules from degrading. May contain tissue/DNA of other taxa, e.g. endosymbionts, pathogens, destruents |
Examples | leaf, muscle, kidney, stem, blood |
Reference | Droege,G. et al. (2016), https://doi.org/10.1093/database/baw125 |
DwC:materialSample | tissue |
ABCD:KindOfUnit | tissue |
GGBN:materialSampleType | tissue |
Comment | Examples in DwC are more equal to what in terms of GGBN is preparationType; the GGBN term "materialSampleType" has been developed to work with DwC as ABCD already has an appropriate term so not needed there but "KindOfUnit" is not used by DwC; GGBN developed a preparation vocabulary including date, person, method, materials and type of preparation, hence the more precise term "preparationType"; Any tissue or specimen is also an environmental for other organisms, but calling everything "environmental sample" doesn't make any sense; it is the decision of the curator of the collection how to categorize their samples |
Similar to the existing mapping DwC-ABCD and DwC-MIxs, there is a mapping between ABCD and MIxS needed. The new MIxS 6 version should be taken into account.
Interestingly and somewhat confusingly, the GSC doesn't seem to want to include licensing information in its MIxS list (see here)
The DwC reuse of the dc:license seems wise in most cases.
Other relevant terms include:
dcterms:accessRights
dcterms:references
dcterms:rights
dcterms:rightsHolder
We should include the recommendation to use these DC classes in our GBWG TG report for managing omics data across the UNESCO/OBIS/GBIF digital ecosystem, to allow them to comply with the "R" in FAIR.
Fields like this will become more important as Nagoya and other regulatory frameworks come into play around digital sequence information.
Field | Value |
---|---|
subject_id | http://rs.tdwg.org/dwc/terms/minimumDistanceAboveSurfaceInMeters |
subject_definition | The lesser distance in a range of distance from a reference surface in the vertical direction, in meters. Use positive values for locations above the surface, negative values for locations below. If depth measures are given, the reference surface is the location given by the depth, otherwise the reference surface is the location given by the elevation. |
subject_usage_notes | |
subject_examples | -1.5 (below the surface). 4.2 (above the surface). For a 1.5 meter sediment core from the bottom of a lake (at depth 20m) at 300m elevation: verbatimElevation: 300m minimumElevationInMeters: 300 , maximumElevationInMeters: 300 , verbatimDepth: 20m , minimumDepthInMeters: 20 , maximumDepthInMeters: 20 , minimumDistanceAboveSurfaceInMeters: 0 , maximumDistanceAboveSurfaceInMeters: -1.5 . |
predicate_id | skos:narrowMatch |
object_id | None given |
object_label | alt |
object definition | Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth’s surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
comment | A range of altitude can be captured in the combination of the terms dwc:minimumDistanceAboveSurfaceInMeters and dwc:maximumDistanceAbveSurfaceInMeters. If a single value is given, the same value should be used in both DwC terms. |
and
Field | Value |
---|---|
subject_id | http://rs.tdwg.org/dwc/terms/maximumDistanceAboveSurfaceInMeters |
subject_definition | The greater distance in a range of distance from a reference surface in the vertical direction, in meters. Use positive values for locations above the surface, negative values for locations below. If depth measures are given, the reference surface is the location given by the depth, otherwise the reference surface is the location given by the elevation. |
subject_usage_notes | |
subject_examples | -1.5 (below the surface). 4.2 (above the surface). For a 1.5 meter sediment core from the bottom of a lake (at depth 20m) at 300m elevation: verbatimElevation: 300m minimumElevationInMeters: 300 , maximumElevationInMeters: 300 , verbatimDepth: 20m , minimumDepthInMeters: 20 , maximumDepthInMeters: 20 , minimumDistanceAboveSurfaceInMeters: 0 , maximumDistanceAboveSurfaceInMeters: -1.5 . |
predicate_id | skos:narrowMatch |
object_id | None given |
object_label | alt |
object definition | Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth’s surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
comment | A range of altitude can be captured in the combination of the terms dwc:minimumDistanceAboveSurfaceInMeters and dwc:maximumDistanceAbveSurfaceInMeters. If a single value is given, the same value should be used in both DwC terms. |
Field | Value |
---|---|
subject_id | http://rs.tdwg.org/dwc/terms/sampleSizeValue |
subject_definition | A numeric value for a measurement of the size (time duration, length, area, or volume) of a sample in a sampling event. |
subject_usage_notes | A sampleSizeValue must have a corresponding sampleSizeUnit. |
subject_examples | 5 for sampleSizeValue with metre for sampleSizeUnit. |
predicate_id | skos:broadMatch |
object_id | MIXS:0000001 |
object_label | samp_size |
object definition | Amount or size of sample (volume, mass or area) that was collected |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
comment | dwc:sampleSizeValue requires the units of the measure to be given in dwc:sampleSizeUnit. |
and
Field | Value |
---|---|
subject_id | http://rs.tdwg.org/dwc/terms/sampleSizeUnit |
subject_definition | The unit of measurement of the size (time duration, length, area, or volume) of a sample in a sampling event. |
subject_usage_notes | A sampleSizeUnit must have a corresponding sampleSizeValue, e.g., 5 for sampleSizeValue with metre for sampleSizeUnit. |
subject_examples | minute , hour , day , metre , square metre , cubic metre |
predicate_id | skos:broadMatch |
object_id | MIXS:0000001 |
object_label | samp_size |
object definition | Amount or size of sample (volume, mass or area) that was collected |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
comment | dwc:sampleSizeUnit must accompany the measure given in dwc:sampleSizeValue. |
Hi @cmungall,
I had a look at the Simple Standard for Sharing Ontology Mappings (SSSOM), which looks like a good option to perform semantically precise mapping of related DwC and MIxS terms (I've had an exemplary first go at this below).
Would you think that SSSOM could be a suitable option for this? Or should I be looking at some other guides?
Best,
Raïssa
subject_id | subject_label | subject_category | predicate_id | object_id | object_label | object_category | match_type | comment |
---|---|---|---|---|---|---|---|---|
dwc:country | Country | DwC Location | skos:closeMatch | MIXS:0000010 | geographic location (country and/or sea, region) | MIxS checklist | HumanCurated | DwC term expects the name of a country, while the MIxS term may either be the name of a country or a sea |
dwc:decimalLatitude | Decimal Latitude | DwC Location | skos:narrowMatch / ro:concretizes [RO:0000059] | MIXS:0000009 | geographic location (latitude and longitude) | MIxS checklist | HumanCurated | DwC term only covers part of the MIxS term (latitude) and specifies the writing convention |
dwc:decimalLongitude | Decimal Longitude | DwC Location | skos:narrowMatch / ro:concretizes [RO:0000059] | MIXS:0000009 | geographic location (latitude and longitude) | MIxS checklist | HumanCurated | DwC term only covers part of the MIxS term (longitude) and specifies the writing convention |
While most MIxS terms specify a constrained value syntax, many of the mapped DwC terms are "verbatim".
We will have to consider this in addition to the definitions when choosing mapping predicates. We will add a column to the mapping spreadsheet to capture this.
Moreover, the mapping predicates may change depending on the direction of the mapping (e.g. see issue #15).
Example
For MIxS elevation the value syntax is constrained to be {float}{unit}, however for verbatimElevation it could be anything, e.g. 1 m 5 cm, so {float}{unit}{float}{unit}, etc.
Here, for taking MIxS into DwC skos:exactMatch is fine, however, if the mapping goes from DwC to MIxS there is no guarantee that the value syntax pattern will be matched. We are currently mapping in the direction of DwC to MIxS, so it would be a skos:broadMatch (because the subject is DwC and the object is MIxS, the DwC would always be broader because there could be a wider range of syntax coming from verbatim)
CALeDNA is an important GGBN member and holds a big collection of environmental samples. The publication of those sample data is due in 2021 and currently done with ABCD-GGBN-Enviro. This use cae will be used for discussion in the IG.
Field | Value |
---|---|
Term | Genomic DNA |
Definition | The physical result of DNA extraction of a tissue sample containing DNA from a single taxon. Usually not completely consumed during sequencing and deposited in a biodiversity biobank |
Examples | gDNA |
Reference | Droege,G. et al. (2016), https://doi.org/10.1093/database/baw125 |
DwC:materialSample | DNA |
ABCD:KindOfUnit | DNA |
GGBN:materialSampleType | DNA |
DwC:preparations | tbd |
ABCD:preparationType | ABCD uses GGBN term |
GGBN:preparationType | gDNA |
Comments | GGBN developed a preparation vocabulary including date, person, method, materials and type of preparation, hence the new more precise term "preparationType" |
or
Field | Value |
---|---|
Term | Organismal DNA |
Definition | Refers to DNA sampled directly from the organism through whole organism collection (e.g. invertebrates), swabbing, blood sampling, clipping etc. Usually high concentration and non-degraded. The location of the organism at the time of sampling is definitively known. Overall there are fewer uncertainties than for eDNA. |
Examples | gDNA |
Reference | https://www.naturemetrics.co.uk/info-hub/edna-glossary/ |
Field | Value |
---|---|
subject_id | http://data.ggbn.org/schemas/ggbn/terms/volume |
subject_definition | Volume of sample |
subject_usage_notes | this element can be used for DNA or tissue samples, in ABCD this element has stringUnit as attribute (example µl, ml), in DarwinCore this element has to be used together with ggbn:volumeUnit |
subject_examples | 30, 150 |
predicate_id | skos:narrowMatch |
object_id | MIXS:0000001 |
object_label | samp_size |
object definition | Amount or size of sample (volume, mass or area) that was collected |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
and
Field | Value |
---|---|
subject_id | http://data.ggbn.org/schemas/ggbn/terms/weight |
subject_definition | Weight of sample |
subject_usage_notes | this element can be used for DNA or tissue samples, in ABCD this element has stringUnit as attribute (example ng, mg, g), in DarwinCore this element has to be used together with ggbn:weightUnit |
subject_examples | 10 |
predicate_id | skos:narrowMatch |
object_id | MIXS:0000001 |
object_label | samp_size |
object definition | Amount or size of sample (volume, mass or area) that was collected |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
Field | Value |
---|---|
subject_id | http://data.ggbn.org/schemas/ggbn/terms/primerName |
subject_definition | Name of primer used for this amplification, cloning, or single read |
subject_usage_notes | can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerNameForward or ggbn:primerNameReverse |
subject_examples | |
predicate_id | skos:narrowMatch |
object_id | MIXS:0000046 |
object_label | pcr_primers |
object definition | PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
or {
Field | Value |
---|---|
subject_id | http://data.ggbn.org/schemas/ggbn/terms/primerNameForward |
subject_definition | Name of primer used for this amplification, cloning, or single read |
subject_usage_notes | only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerName |
subject_examples | |
predicate_id | skos:narrowMatch |
object_id | MIXS:0000046 |
object_label | pcr_primers |
object definition | PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
and
Field | Value |
---|---|
subject_id | http://data.ggbn.org/schemas/ggbn/terms/primerNameReverse |
subject_definition | Name of primer used for this amplification, cloning, or single read |
subject_usage_notes | only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerName |
subject_examples | |
predicate_id | skos:narrowMatch |
object_id | MIXS:0000046 |
object_label | pcr_primers |
object definition | PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
}
and
Field | Value |
---|---|
subject_id | http://data.ggbn.org/schemas/ggbn/terms/primerSequence |
subject_definition | DNA sequence of the primer (A,T,G,C; 5' to 3') |
subject_usage_notes | can be used for ABCD implementation; for Darwin Core-Archive implementation please use ggbn:primerSequenceForward or ggbn:primerSequenceReverse |
subject_examples | |
predicate_id | skos:narrowMatch |
object_id | MIXS:0000046 |
object_label | pcr_primers |
object definition | PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
or {
Field | Value |
---|---|
subject_id | http://data.ggbn.org/schemas/ggbn/terms/primerSequenceForward |
subject_definition | DNA sequence of the primer (A,T,G,C; 5' to 3') |
subject_usage_notes | only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerSequence |
subject_examples | |
predicate_id | skos:narrowMatch |
object_id | MIXS:0000046 |
object_label | pcr_primers |
object definition | PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
and
Field | Value |
---|---|
subject_id | http://data.ggbn.org/schemas/ggbn/terms/primerSequenceReverse |
subject_definition | DNA sequence of the primer (A,T,G,C; 5' to 3') |
subject_usage_notes | only for Darwin Core-Archive implementation! For ABCD implementation please use ggbn:primerSequence |
subject_examples | |
predicate_id | skos:narrowMatch |
object_id | MIXS:0000046 |
object_label | pcr_primers |
object definition | PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
}
Field | Value |
---|---|
subject_id | http://rs.tdwg.org/dwc/terms/verbatimElevation |
subject_definition | The original description of the elevation (altitude, usually above sea level) of the Location. |
subject_usage_notes | |
subject_examples | 100-200 m |
predicate_id | skos:broadMatch |
object_id | MIXS:0000093 |
object_label | elev |
object definition | Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
comment | Going from MIxS to Darwin Core, the predicate would be skos:exactMatch, as the pattern in MIxS will always be acceptable on the Darwin Core side. |
Field | Value |
---|---|
subject_id | http://rs.tdwg.org/dwc/terms/samplingProtocol |
subject_definition | The name of, reference to, or description of the method or protocol used during an Event. |
subject_usage_notes | |
subject_examples | UV light trap , mist net , bottom trawl , ad hoc observation , point count , Penguins from space: faecal stains reveal the location of emperor penguin colonies, https://doi.org/10.1111/j.1466-8238.2009.00467.x, Takats et al. 2001. Guidelines for Nocturnal Owl Monitoring in North America. Beaverhill Bird Observatory and Bird Studies Canada, Edmonton, Alberta. 32 pp., http://www.bsc-eoc.org/download/Owl.pdf |
predicate_id | skos:broadMatch |
object_id | MIXS:0000002 |
object_label | samp_collect_device |
object definition | The method or device employed for collecting the sample |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
comment | dwc:samplingProtocol covers both of the concepts samp_collect_device and samp_collect_process. |
Field | Value |
---|---|
subject_id | http://rs.tdwg.org/dwc/terms/associatedTaxa |
subject_definition | A list (concatenated and separated) of identifiers or names of taxa and their associations with the Occurrence. |
subject_usage_notes | |
subject_examples | "host":"Quercus alba", "parasitoid of":"Cyclocephala signaticollis" | "predator of":"Apis mellifera" |
predicate_id | skos:relatedMatch |
object_id | MIXS:0000248 |
object_label | host_common_name |
object definition | Common name of the host, e.g. Human |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
comment | The MIxS term is from MIxS envPac host-associated. Potentially, the predicate_id here can be skos:narrowMatch since the MIxS term explicitly defines a host relationship, whereas the DwC term can be used for any species-species interaction. |
Field | Value |
---|---|
Term | Ancient Environmental DNA |
Definition | The physical result of DNA extraction of an environmental sample older than 100 years (e.g. gut) containing DNA of multiple taxa. Usually completely processed during sequencing |
Examples | tbd |
Reference | Droege,G. et al. (2016), https://doi.org/10.1093/database/baw125 |
DwC:materialSample | DNA |
ABCD:KindOfUnit | DNA |
GGBN:materialSampleType | DNA |
DwC:preparations | tbd |
ABCD:preparationType | ABCD uses GGBN term |
GGBN:preparationType | tbd |
Comments | GGBN developed a preparation vocabulary including date, person, method, materials and type of preparation, hence the new more precise term "preparationType" |
Field | Value |
---|---|
subject_id | http://rs.tdwg.org/dwc/terms/verbatimDepth |
subject_definition | The original description of the depth below the local surface. |
subject_usage_notes | |
subject_examples | 100-200 m |
predicate_id | skos:narrowMatch |
object_id | MIXS:0000018 |
object_label | depth |
object definition | Depth is defined as the vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
comment | In Darwin Core, according to best practices, depth is measured in water from an air-water surface, while in other media the corresponding terms are dwc:minimumDistanceAboveSurfaceInMeters and dwc:maximumDistanceAboveSurfaceInMeters, where the values would be negative for depth. Thus, for a sediment at the bottom of a lake, there would be an elevation of the lake surface, the depth of the top of the sediment in the lake, and minimum and maximum distances below the sediment surface within which a sample was taken. |
or
Field | Value |
---|---|
subject_id | http://rs.tdwg.org/dwc/terms/minimumDistanceAboveSurfaceInMeters |
subject_definition | The lesser distance in a range of distance from a reference surface in the vertical direction, in meters. Use positive values for locations above the surface, negative values for locations below. If depth measures are given, the reference surface is the location given by the depth, otherwise the reference surface is the location given by the elevation. |
subject_usage_notes | |
subject_examples | -1.5 (below the surface). 4.2 (above the surface). For a 1.5 meter sediment core from the bottom of a lake (at depth 20m) at 300m elevation: verbatimElevation: 300m minimumElevationInMeters: 300 , maximumElevationInMeters: 300 , verbatimDepth: 20m , minimumDepthInMeters: 20 , maximumDepthInMeters: 20 , minimumDistanceAboveSurfaceInMeters: 0 , maximumDistanceAboveSurfaceInMeters: -1.5 . |
predicate_id | skos:narrowMatch |
object_id | MIXS:0000018 |
object_label | depth |
object definition | Depth is defined as the vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
comment | In Darwin Core, according to best practices, depth is measured in water from an air-water surface, while in other media the corresponding terms are dwc:minimumDistanceAboveSurfaceInMeters and dwc:maximumDistanceAboveSurfaceInMeters, where the values would be negative for depth. Thus, for a sediment at the bottom of a lake, there would be an elevation of the lake surface, the depth of the top of the sediment in the lake, and minimum and maximum distances below the sediment surface within which a sample was taken. |
and
Field | Value |
---|---|
subject_id | http://rs.tdwg.org/dwc/terms/maximumDistanceAboveSurfaceInMeters |
subject_definition | The greater distance in a range of distance from a reference surface in the vertical direction, in meters. Use positive values for locations above the surface, negative values for locations below. If depth measures are given, the reference surface is the location given by the depth, otherwise the reference surface is the location given by the elevation. |
subject_usage_notes | |
subject_examples | -1.5 (below the surface). 4.2 (above the surface). For a 1.5 meter sediment core from the bottom of a lake (at depth 20m) at 300m elevation: verbatimElevation: 300m minimumElevationInMeters: 300 , maximumElevationInMeters: 300 , verbatimDepth: 20m , minimumDepthInMeters: 20 , maximumDepthInMeters: 20 , minimumDistanceAboveSurfaceInMeters: 0 , maximumDistanceAboveSurfaceInMeters: -1.5 . |
predicate_id | skos:narrowMatch |
object_id | MIXS:0000018 |
object_label | depth |
object definition | Depth is defined as the vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
comment | In Darwin Core, according to best practices, depth is measured in water from an air-water surface, while in other media the corresponding terms are dwc:minimumDistanceAboveSurfaceInMeters and dwc:maximumDistanceAboveSurfaceInMeters, where the values would be negative for depth. Thus, for a sediment at the bottom of a lake, there would be an elevation of the lake surface, the depth of the top of the sediment in the lake, and minimum and maximum distances below the sediment surface within which a sample was taken. |
Hey,
I am wondering if there is any documentation on how to map BIOM format (OTU tables) to Darwin Core?
I have seen some example like BIOWIDE eDNA Fungi dataset which has OTU's information, so there should be some degree of mapping between information from BIOM formatted OTU tables to Darwin Core right?
Thanks so much!
A few years ago all MIxS terms (as well as DwC, ABCD and GGBN) have been added to terms.tdwg.wiki to have them all in one place. This platform won't last forever, the standards are maintained elsewhere.
For MIxS the URI http://gensc.org/ns/mixs/TERMNAME is used, see e.g. https://terms.tdwg.org/wiki/mixs:samp_size
Please note, that this URI resolves to terms.tdwg.org! Depending on decisions for MIxS6.0 this might need to be changed by GSC.
Field | Value |
---|---|
subject_id | http://rs.tdwg.org/dwc/terms/verbatimCoordinates |
subject_definition | The verbatim original spatial coordinates of the Location. The coordinate ellipsoid, geodeticDatum, or full Spatial Reference System (SRS) for these coordinates should be stored in verbatimSRS and the coordinate system should be stored in verbatimCoordinateSystem. |
subject_usage_notes | |
subject_examples | 41 05 54S 121 05 34W, 17T 630000 4833400 |
predicate_id | skos:broadMatch |
object_id | MIXS:0000009 |
object_label | lat_lon |
object definition | The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
comment | The Coordinate Reference System "epsg:4326" must be provided explicitly in dwc:verbatimSRS in order for the mapping to be complete. |
GGBN is using ABCD2.1 as an interim solution between ABCD2.06 and ABCD3.0.
In ABCD2.1 the following MIxS terms have been included and hence need no mapping (they will be included in ABCD3.0 as well):
In GGBN v1 the following MIxS terms have been included and hence need no mapping:
Field | Value |
---|---|
subject_id | http://rs.tdwg.org/dwc/terms/materialSampleID |
subject_definition | An identifier for the MaterialSample (as opposed to a particular digital record of the material sample). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the materialSampleID globally unique. |
subject_usage_notes | Recommended best practice is to use a persistent, globally unique identifier. |
subject_examples | 06809dc5-f143-459a-be1a-6f03e63fc083 |
predicate_id | skos:exactMatch |
object_id | MIXS:0000026 |
object_label | source_mat_id |
object definition | A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
comment |
Field | Value |
---|---|
subject_id | http://rs.tdwg.org/dwc/terms/samplingProtocol |
subject_definition | The name of, reference to, or description of the method or protocol used during an Event. |
subject_usage_notes | |
subject_examples | UV light trap , mist net , bottom trawl , ad hoc observation , point count , Penguins from space: faecal stains reveal the location of emperor penguin colonies, https://doi.org/10.1111/j.1466-8238.2009.00467.x, Takats et al. 2001. Guidelines for Nocturnal Owl Monitoring in North America. Beaverhill Bird Observatory and Bird Studies Canada, Edmonton, Alberta. 32 pp., http://www.bsc-eoc.org/download/Owl.pdf |
predicate_id | skos:broadMatch |
object_id | MIXS:0000016 |
object_label | samp_mat_process |
object definition | Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
comment | dwc:samplingProtocol covers both of the concepts samp_collect_device and samp_collect_process. |
Field | Value |
---|---|
Term | Environmental DNA |
Definition | The physical result of DNA extraction of an environmental sample containing DNA of multiple taxa. Often completely consumed during sequencing |
Examples | eDNA |
Reference | Droege,G. et al. (2016), https://doi.org/10.1093/database/baw125 |
DwC:materialSample | DNA |
ABCD:KindOfUnit | DNA |
GGBN:materialSampleType | DNA |
DwC:preparations | tbd |
ABCD:preparationType | ABCD uses GGBN term |
GGBN:preparationType | gDNA |
Comment | GGBN developed a preparation vocabulary including date, person, method, materials and type of preparation, hence the new more precise term "preparationType" |
or
Field | Value |
---|---|
Term | Environmental DNA |
Definition | DNA from an environmental sample, e.g. soil, water, air or host organism. An often used definition is that environmental DNA is the genetic material (DNA) obtained from environmental samples without any obvious evidence of biological source material |
Examples | eDNA |
Reference | GBIF guide, https://doi.org/10.35035/doc-vf1a-nr22; Thomsen and Willerslev 2015, https://doi.org/10.1016/j.biocon.2014.11.019 |
or
Field | Value |
---|---|
Term | Environmental DNA |
Definition | Refers to DNA deposited in the environment through excretion, shedding, mucous secretions, saliva etc. This can be collected in environmental samples (e.g. water, sediment) and used to identify the organisms that it originated from. eDNA in water is broken down by environmental processes over a period of days to weeks. It can travel some distance from the point at which it was released from the organism, particularly in running water. eDNA in soil can bind to organic particles and persist for a very long time (sometimes hundreds or thousands of years). eDNA is sampled in low concentrations and can be degraded (i.e. broken into short fragments), which limits the analysis options. |
Examples | eDNA |
Reference | https://www.naturemetrics.co.uk/info-hub/edna-glossary/ |
or
Field | Value |
---|---|
Term | Environmental DNA |
Definition | DNA that is collected from an environment, rather than from an organism. Most commonly, this term is used to describe DNA that is no longer located in living cells (e.g. excreted DNA and DNA within cellular debris), although frequently it is also used to describe DNA extracted from biotic media (e.g. hair, blood, scat, fur). Environmental DNA is typically derived from nuclear and mitochondrial DNA and, generally, mitochondrial DNA is preferred for species detection because it is more abundant than nuclear DNA, and more sequence data are available. |
Examples | eDNA |
Reference | https://edna.epri.com/glossary.html |
or
Field | Value |
---|---|
Term | Environmental DNA |
Definition | Environmental DNA refers to DNA that can be extracted from environmental samples (such as soil, water or air), without first isolating any target organisms. It is characterized by a complex mixture of genomic DNA from many different organisms and by possible degradation (i.e. DNA molecules are cut into small fragments). Total eDNA contains cellular DNA originating from living cells or organisms, and extracellular DNA (Levy‐Booth et al. 2007; Pietramellara et al. 2009) resulting from natural cell death and subsequent destruction of cell structure. |
Examples | eDNA |
Reference | Taberlet et al. 2012: Environmental DNA, https://doi.org/10.1111/j.1365-294X.2012.05542.x |
Hi @timrobertson100 and @thomasstjerne,
Looking at the MIxS-relevant part of this collection of extensions that GBIF offers, I noted that they vary in scope and that some focus on MIxS, while others also cover parts of GGBN and MIQE, however I'm wondering how they relate to each other.
Are these extensions sequential or are they independent?
And how do they, including GBIF’s DNA derived data extension relate to the 2012 extension built by @tucotuco et al.?
Best,
Raïssa
Field | Value |
---|---|
subject_id | http://data.ggbn.org/schemas/ggbn/terms/amplificationMethod |
subject_definition | Method used for amplification/PCR |
subject_usage_notes | |
subject_examples | |
predicate_id | skos:exactMatch |
object_id | MIXS:0000038 |
object_label | nucl_acid_amp |
object definition | A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids |
object source | https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx |
Field | Value |
---|---|
Term | Material Sample |
Definition | The physical result of a sampling (or subsampling) event. In biological collections, the material sample is typically collected, and either preserved or destructively processed. Might contain DNA/RNA, but doesn't have to. "Genomic Sample" is a subset of Material Samples containing molecular properties. |
Examples | specimen, culture, DNA, RNA, tissue, environmental sample (or eSample) |
Reference | DwC, https://dwc.tdwg.org/terms/; Droege,G. et al. (2016), https://doi.org/10.1093/database/baw125 |
DwC:basisOfRecord | MaterialSample |
ABCD:RecordBasis | MaterialSample |
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