GenomicsStandardsConsortium
Geo location usage guidance
The current description of the geo-location variable is
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)
This is fine but... do we (GSC or DarwinCore) supply any advice/guidance on which location should be used for things that have been moved. e.g. plants originally collected in the wild but been grown for many years in a botanical garden somewhere, or zoo animals originally from the wild, or wild fish/coral now kept in aquariums? For metagenome sequences I can see that the current location is appropriate, but for the genome of the sample should we use the original or the transplanted location? Do we need a way to specify which has been given?
We don't have any guidance so far. I remember that this issue was discussed in the context of occurrences in GBIF (tigers in UK). I'm not sure what the outcome of that is. Perhaps @jdeck88 or @tucotuco could comment what their guidance is and we can try to adopt that.
Bob Robbins liked to ask: what is the difference between an ant transporting a leaf to an underground hole and a monkey putting a cat in a box?
Philosophical ponderings aside, Darwin Core has a useful term establishmentMeans (http://rs.tdwg.org/dwc/terms/#establishmentMeans) that indicates how the occurrence (or in our case, sample) became established at the location that is marked by the country, location, or coordinates.
John
On Thu, Jun 21, 2018 at 7:32 AM pyilmaz [email protected] wrote:
We don't have any guidance so far. I remember that this issue was discussed in the context of occurrences in GBIF (tigers in UK). I'm not sure what the outcome of that is. Perhaps @jdeck88 https://github.com/jdeck88 or @tucotuco https://github.com/tucotuco could comment what their guidance is and we can try to adopt that.
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If this is still an important term, I suggest adopting the new DwC terms for research and management of alien species. The manuscript is currently under review, but when finalized, the new changes will be:
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Introducing a controlled vocabulary for the existing Darwin Core term dwc:establishmentMeans
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Promoting the pathway term from the Darwin Core Invasive Species Pathways extension as a new Darwin Core term dwc:pathway
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Adopting a new Darwin Core term dwc:degreeOfEstablishment with an associated controlled vocabulary
A lot of effort and community input went into this, so no reason for GSC to reinvent the wheel.
I will update here when the paper is accepted and the standard is updated.
For MIxS 6, we can leave this as is, but work with the MIxS/DwC coordination group to clarify location terms.
This terms is for a place name. We have lat and long terms.
Will need to clarify between where original sample was taken in the wild and where a sample was taken in a lab (if that info is relevant).
@pbuttigieg
see also : https://github.com/GenomicsStandardsConsortium/mixs/issues/528
Comparison of the country terms from INSDC and GAZ
INSDC - removed oceans and seas) GAZ - used the country subset OWL used the straight labels and no synonyms (parsed used pronto, so could add that at a later time)
woollard@JTJG77DMX2 source % time ./compareINSDC_countries_w_gaz.py INFO - INSDC oceans={'Indian Ocean', 'Arctic Ocean', 'Southern Ocean', 'North Sea', 'Tasman Sea', 'Pacific Ocean', 'Ross Sea', 'Atlantic Ocean', 'Baltic Sea', 'Mediterranean Sea'}
INFO - Load the GAZ ontology from its URL
GAZ country set total:=202 INSDC country set total:=270 Overlapping countries total=184 ['Afghanistan', 'Albania', 'Algeria', 'Andorra', 'Angola', 'Antarctica', 'Antigua and Barbuda', 'Argentina', 'Armenia', 'Australia', 'Austria', 'Azerbaijan', 'Bahamas', 'Bahrain', 'Bangladesh', 'Barbados', 'Belarus', 'Belgium', 'Belize', 'Benin', 'Bhutan', 'Bolivia', 'Bosnia and Herzegovina', 'Botswana', 'Brazil', 'Bulgaria', 'Burkina Faso', 'Burundi', 'Cambodia', 'Cameroon', 'Canada', 'Cape Verde', 'Central African Republic', 'Chad', 'Chile', 'China', 'Colombia', 'Comoros', 'Costa Rica', "Cote d'Ivoire", 'Croatia', 'Cuba', 'Cyprus', 'Democratic Republic of the Congo', 'Denmark', 'Djibouti', 'Dominica', 'Dominican Republic', 'Ecuador', 'Egypt', 'El Salvador', 'Equatorial Guinea', 'Eritrea', 'Estonia', 'Eswatini', 'Ethiopia', 'Fiji', 'Finland', 'France', 'Gabon', 'Gambia', 'Georgia', 'Germany', 'Ghana', 'Gibraltar', 'Greece', 'Grenada', 'Guatemala', 'Guinea', 'Guinea-Bissau', 'Guyana', 'Haiti', 'Honduras', 'Hungary', 'Iceland', 'India', 'Indonesia', 'Iran', 'Iraq', 'Israel', 'Italy', 'Jamaica', 'Japan', 'Jordan', 'Kazakhstan', 'Kenya', 'Kiribati', 'Kosovo', 'Kuwait', 'Kyrgyzstan', 'Laos', 'Latvia', 'Lebanon', 'Lesotho', 'Liberia', 'Libya', 'Liechtenstein', 'Lithuania', 'Luxembourg', 'Madagascar', 'Malawi', 'Malaysia', 'Mali', 'Malta', 'Marshall Islands', 'Mauritania', 'Mauritius', 'Mexico', 'Moldova', 'Monaco', 'Mongolia', 'Montenegro', 'Morocco', 'Mozambique', 'Myanmar', 'Namibia', 'Nauru', 'Nepal', 'Netherlands', 'New Zealand', 'Nicaragua', 'Niger', 'Nigeria', 'North Korea', 'Norway', 'Oman', 'Pakistan', 'Palau', 'Panama', 'Papua New Guinea', 'Paraguay', 'Peru', 'Philippines', 'Poland', 'Portugal', 'Qatar', 'Romania', 'Russia', 'Rwanda', 'Saint Lucia', 'Saint Vincent and the Grenadines', 'Samoa', 'San Marino', 'Sao Tome and Principe', 'Saudi Arabia', 'Senegal', 'Serbia', 'Seychelles', 'Sierra Leone', 'Singapore', 'Slovenia', 'Solomon Islands', 'Somalia', 'South Korea', 'Spain', 'Sri Lanka', 'Sudan', 'Suriname', 'Sweden', 'Switzerland', 'Syria', 'Taiwan', 'Tajikistan', 'Tanzania', 'Thailand', 'Timor-Leste', 'Togo', 'Tonga', 'Trinidad and Tobago', 'Tunisia', 'Turkey', 'Turkmenistan', 'Tuvalu', 'Uganda', 'Ukraine', 'United Arab Emirates', 'United Kingdom', 'Uruguay', 'Uzbekistan', 'Vanuatu', 'Venezuela', 'Yemen', 'Zambia', 'Zimbabwe']
countries unique in GAZ total: 18 ['Brunei Darussalam', 'Czech Republic', 'England', 'Island Nation', 'Macedonia', 'Northern Ireland', 'Palestine', 'Republic of Congo', 'Republic of Ireland', 'Republic of Maldives', 'Republic of South Africa', 'Saint Kitts-Nevis', 'Scotland', 'Slovak Republic', 'United States of America', 'Vatican City', 'Vietnam', 'Wales']
countries unique in INSDC total: 86 ['American Samoa', 'Anguilla', 'Aruba', 'Ashmore and Cartier Islands', 'Baker Island', 'Bassas da India', 'Bermuda', 'Borneo', 'Bouvet Island', 'British Virgin Islands', 'Brunei', 'Cayman Islands', 'Christmas Island', 'Clipperton Island', 'Cocos Islands', 'Cook Islands', 'Coral Sea Islands', 'Curacao', 'Czechia', 'Europa Island', 'Falkland Islands (Islas Malvinas)', 'Faroe Islands', 'French Guiana', 'French Polynesia', 'French Southern and Antarctic Lands', 'Gaza Strip', 'Glorioso Islands', 'Greenland', 'Guadeloupe', 'Guam', 'Guernsey', 'Heard Island and McDonald Islands', 'Hong Kong', 'Howland Island', 'Ireland', 'Isle of Man', 'Jan Mayen', 'Jarvis Island', 'Jersey', 'Johnston Atoll', 'Juan de Nova Island', 'Kerguelen Archipelago', 'Kingman Reef', 'Line Islands', 'Macau', 'Maldives', 'Martinique', 'Mayotte', 'Micronesia, Federated States of', 'Midway Islands', 'Montserrat', 'Navassa Island', 'New Caledonia', 'Niue', 'Norfolk Island', 'North Macedonia', 'Northern Mariana Islands', 'Palmyra Atoll', 'Paracel Islands', 'Pitcairn Islands', 'Puerto Rico', 'Republic of the Congo', 'Reunion', 'Saint Barthelemy', 'Saint Helena', 'Saint Kitts and Nevis', 'Saint Martin', 'Saint Pierre and Miquelon', 'Sint Maarten', 'Slovakia', 'South Africa', 'South Georgia and the South Sandwich Islands', 'South Sudan', 'Spratly Islands', 'State of Palestine', 'Svalbard', 'Tokelau', 'Tromelin Island', 'Turks and Caicos Islands', 'USA', 'Viet Nam', 'Virgin Islands', 'Wake Island', 'Wallis and Futuna', 'West Bank', 'Western Sahara'] ./compareINSDC_countries_w_gaz.py 0.13s user 0.06s system 34% cpu 0.561 total woollard@JTJG77DMX2 source %
