tag:blogger.com,1999:blog-2326624813533383062.post1831026566307156275..comments2024-01-29T12:53:16.114+01:00Comments on Developer Blog: Updating the GBIF BackboneTim Robertsonhttp://www.blogger.com/profile/07889700598656669041noreply@blogger.comBlogger25125tag:blogger.com,1999:blog-2326624813533383062.post-25491833033559356592016-04-22T03:58:37.786+02:002016-04-22T03:58:37.786+02:00Chilodontidae (1): Mollusca > Gastropoda > V...Chilodontidae (1): Mollusca > Gastropoda > Vetigastropoda<br />Chilodontidae (2): Chordata > Vertebrata > Gnathostomata > Osteichthyes > Actinopterygii > Neopterygii > Teleostei > Characiformes<br /><br />* Tony note: Chilodontidae Wenz, 1938 (Mollusca) is currently an unreplaced junior homonym of Chilodontidae Eigenmann, 1912 (Actinopterygii), needs replacement name and/or referral to ICZN for resolution.<br /><br />Megascolecidae (1): Annelida > Clitellata > Oligochaeta > Tubificida<br />Megascolecidae (2): Annelida > Clitellata > Oligochaeta > Metagynophora > Opistophora<br /><br />* Tony note: I believe this is a duplicate entry (same family, different placement). Family authorship is Rosa, 1891.<br /><br />Hydridae (1): Cnidaria > Medusozoa > Hydrozoa > Hydroidolina > Anthoathecata<br />Hydridae (2): Mollusca > Bivalvia > Autobranchia > Heteroconchia > Unionida<br /><br />* Tony note: Hydridae Dana, 1846 is a valid family in Cnidaria. "Hydridae" in Mollusca (Unionida) appears to be a misspelling of Hyriidae Swainson, 1840 (type genus is Hyria Lamarck, 1819).<br /><br />Poraniidae (1): Echinodermata > Asterozoa > Asteroidea > Valvatacea<br />Poraniidae (2): Echinodermata > Asterozoa > Asteroidea > Valvatacea > Valvatida<br /><br />* Tony note: I believe this is a duplicate entry (same family, different placement). Family authorship is Perrier, 1893.<br /><br />Glossoscolecidae (1): Annelida > Clitellata > Oligochaeta > Tubificida<br />Glossoscolecidae (2): Annelida > Clitellata > Oligochaeta > Metagynophora > Opistophora<br /><br />* Tony note: I believe this is a duplicate entry (same family, different placement). (Family authorship not yet traced)<br /><br />Cepheidae (1): Cnidaria Medusozoa > Scyphozoa > Discomedusae > Rhizostomeae<br />Cepheidae (2): Chelicerata > Arachnida > Acari > Acariformes > Sarcoptiformes<br /><br />* Tony note: Cepheidae Berlese, 1896 (Acariformes) is a junior homonym of Cepheidae L. Agassiz, 1862 (Cnidaria); former is given as synonomym of Compactozetidae Luxton, 1988 in WoRMS (2013).Anonymoushttps://www.blogger.com/profile/00938884035250546549noreply@blogger.comtag:blogger.com,1999:blog-2326624813533383062.post-12355120419420961232016-04-22T03:58:27.142+02:002016-04-22T03:58:27.142+02:00Hi Markus,
I have researched/checked the duplicat...Hi Markus,<br /><br />I have researched/checked the duplicate/potential homonym families from FALO that you list, and my comments are inserted below, prefixed "* Tony:". The list is split into 2 parts on account of the character limit for replies. Hope this helps. Regards - Tony<br /><br />----------------------------<br />Cepolidae (1): Mollusca > Gastropoda > Heterobranchia > Pulmonata > Stylommatophora<br />Cepolidae (2): Chordata > Vertebrata > Gnathostomata > Osteichthyes > Actinopterygii > Neopterygii > Teleostei<br /><br />* Tony note: Cepolidae Ihering, 1909 (Mollusca) is currently an unreplaced junior homonym of Cepolidae Rafinesque, 1815 (Actinopterygii), needs replacement name and/or referral to ICZN for resolution.<br /><br />Lumbricidae (1): Oligochaeta > Tubificida<br />Lumbricidae (2): Oligochaeta > Metagynophora > Opistophora<br /><br />* Tony note: I believe this is a duplicate entry (same family, different placement). Family authorship is Claus, 1876.<br /><br />Odontopharyngidae (1): Nematoda > Chromadorea > Plectia > Rhabditica > Diplogasterida<br />Odontopharyngidae (2): Nematoda > Chromadorea > Plectia > Rhabditica > Rhabditida<br /><br />* Tony note: I believe this is a duplicate entry (same family, different placement). Family authorship is Micoletzky, 1922.<br /><br />Heterocheilidae (1): Insecta > Pterygota > Neoptera > Holometabola > Diptera<br />Heterocheilidae (2): Nematoda > Chromadorea > Plectia > Rhabditica > Spirurida<br /><br />* Tony note: Heterocheilidae McAlpine, 1991 (Diptera) is a junior homonym of Heterocheilidae Railliet & Henry, 1915 (Nematoda), former is given as syn. of Helcomyzidae in WoRMS (2010 version) although incorrectly listed as available/valid in www.diptera.org<br /><br />Lutodrilidae (1): Annelida > Clitellata > Oligochaeta > Metagynophora > Opistophora<br />Lutodrilidae (2): Annelida > Clitellata > Oligochaeta > Metagynophora > Opistophora<br /><br />* Tony note: I believe this is a duplicate entry (same family, different placement). Family authorship is McMahan, 1976.<br /><br />Urostylidae (1): Ciliophora > Intramacronucleata > Spirotrichia > Spirotrichea > Stichotrichia > Urostylida<br />Urostylidae (2): Insecta > Pterygota > Neoptera > Paraneoptera > Hemiptera<br /><br />* Tony note: Urostylidae Bütschli, 1889 (Ciliophora) is a junior homonym of Urostylidae Dallas, 1851 (Hemiptera), however the homonymy has been removed by emendation of Urostylidae Dallas, 1851 (Hemiptera) to Urostylididae by Berger et al. 2001.<br /><br />Sagittariidae (1): Ciliophora > Intramacronucleata > Ventrata > Colpodea > Cyrtolophosidida<br />Sagittariidae (2): Chordata > Vertebrata > Gnathostomata > Tetrapoda > Aves > Neornithes > Neognathae > Neoaves > Accipitriformes<br /><br />* Tony note: Sagittariidae Grandori & Grandori, 1935 (Ciliophora) is currently an unreplaced junior homonym of Sagittariidae Finsch & Hartlaub, 1870 (Aves), needs replacement name and/or referral to ICZN for resolution.Anonymoushttps://www.blogger.com/profile/00938884035250546549noreply@blogger.comtag:blogger.com,1999:blog-2326624813533383062.post-3536834271524007152016-04-20T12:57:17.021+02:002016-04-20T12:57:17.021+02:00We had the Chlorarachniales in our previous backbo...We had the Chlorarachniales in our previous backbone under Protozoa:<br />http://www.gbif.org/species/678<br /><br />As CoL still treats Cercozoa as Protozoa I will add them also there in the Algae dataset. Thanks Tony, that was missing!Anonymoushttps://www.blogger.com/profile/02525336976753861766noreply@blogger.comtag:blogger.com,1999:blog-2326624813533383062.post-85980113465839214472016-04-20T12:48:10.868+02:002016-04-20T12:48:10.868+02:00There are 17 homonym families in the FALO classifi...There are 17 homonym families in the FALO classification - any idea if these are intended to be present?<br /><br />Cepolidae<br />Lumbricidae<br />Odontopharyngidae<br />Heterocheilidae<br />Lutodrilidae<br />Urostylidae<br />Sagittariidae<br />Chilodontidae<br />Megascolecidae<br />Hydridae<br />Poraniidae<br />Glossoscolecidae<br />CepheidaeAnonymoushttps://www.blogger.com/profile/02525336976753861766noreply@blogger.comtag:blogger.com,1999:blog-2326624813533383062.post-31791890658741892882016-04-20T11:07:10.437+02:002016-04-20T11:07:10.437+02:00The new backbone to go live as a simple single CSV...The new backbone to go live as a simple single CSV file Darwin Core archive: http://rs.gbif.org/datasets/backbone/backbone-2016-04-13.csv.gzAnonymoushttps://www.blogger.com/profile/02525336976753861766noreply@blogger.comtag:blogger.com,1999:blog-2326624813533383062.post-49527427563500337462016-04-20T10:33:55.085+02:002016-04-20T10:33:55.085+02:00Thanks Tony, this is useful. Especially since we h...Thanks Tony, this is useful. Especially since we have about 1500 families without any classification yet! Any happy to receive any comments on the algae classification. As we plan to rebuild the backbone now every couple of month we finally can include feedback each timeAnonymoushttps://www.blogger.com/profile/02525336976753861766noreply@blogger.comtag:blogger.com,1999:blog-2326624813533383062.post-55960216035936952352016-04-20T10:19:18.062+02:002016-04-20T10:19:18.062+02:00Thanks!
The null epithet is an issue that should...Thanks! <br /><br />The null epithet is an issue that should be fixed in the new version we build last weekend to go live with today or tomorrow. It was reported here: http://dev.gbif.org/issues/browse/POR-3069<br />I will follow up on mismatching ranks & epithets in this issue: http://dev.gbif.org/issues/browse/POR-3081<br /><br />For synonyms there should never by a direct child in the taxonomy. I have created a new issue http://dev.gbif.org/issues/browse/POR-3080 and will investigate that, thanks!<br /><br />The Index Fungorum version is unfortunately still the old one, yes. We are in touch with both MycoBank and IF now at Kew and hope to get a newer version at some point. But progress has been rather slow so we sticked with the old version for now.Anonymoushttps://www.blogger.com/profile/02525336976753861766noreply@blogger.comtag:blogger.com,1999:blog-2326624813533383062.post-7898975993750567712016-04-18T13:34:53.393+02:002016-04-18T13:34:53.393+02:00I also had a quick look at the new backbone (https...I also had a quick look at the new backbone (https://dl.dropboxusercontent.com/u/457027/nub.txt.zip) and identified a few potentially problematic names - <br /><br />1. 250 taxon names with "taxonRank=SPECIES" but which in fact belong to genus (e.g. 7348906, 7350813, 8232585, etc.)<br />2. 140 taxon names with "taxonRank=VARIETY|FORM" but for which intraspecific epithet is "null" (e.g. 7407832, 8181923 , 8189733, etc.)<br /><br />In addition to that, it seems that there are many taxon names marked as "*SYNONYM|MISAPPLIED" (7,756) or "DOUBTFUL" (4,836) for which there are direct children in the dataset. Is this how GBIF nub taxonomy has been and will be handling such cases or is it something that should ideally be fixed (e.g. parent should be changed to equivalent ACCEPTED name but this has not been done yet)?<br /><br />And finally, I can see that you are also using Index Fungorum as one of the underlying taxonomic sources. Do you use the same 2011 version (http://www.gbif.org/dataset/bf3db7c9-5e5d-4fd0-bd5b-94539eaf9598) or will there be an updated one? Or have there been any discussions about including MycoBank as well?<br /><br />Overall, nice (and enormous load of) work you have done. Very useful service and happy to use it!Anonymoushttps://www.blogger.com/profile/13436201155589731720noreply@blogger.comtag:blogger.com,1999:blog-2326624813533383062.post-35542838336251080282016-04-17T20:49:10.274+02:002016-04-17T20:49:10.274+02:00The problem seems to be Hassler M. (2016). World P...The problem seems to be Hassler M. (2016). World Plants: Synonymic Checklists of the Vascular Plants of the World, which apparently is not a published list, except through the COL. This list has no other online presence and doesn't give the providence of who the taxonomic authority was. I find this disappointing given that so much time and effort that has been put into different taxonomic names lists. It's certainly not GBIF's fault, but I don't think botanists can be proud of the taxonomic name infrastructure we have.Anonymoushttps://www.blogger.com/profile/01823490603450519912noreply@blogger.comtag:blogger.com,1999:blog-2326624813533383062.post-26524542831912526652016-04-17T10:41:09.696+02:002016-04-17T10:41:09.696+02:00Hi Markus,
If you have not seen it, there is a ve...Hi Markus,<br /><br />If you have not seen it, there is a version of Ruggiero et al.'s FALO classification down to family available for download at http://ggi.eol.org/downloads - it is labelled "GGI Family Data". Again if you have not already done so, I would suggest doing a difference report so you can see which families are in FALO and not in the latest GBIF nub, and vice versa, which may give you some discrepancies worth chasing.<br /><br />I had a quick eyeball of the algae list without exhaustive checking, and noted a few items out of place or superfluous, I will send you the things I spotted via separate email.<br /><br />I was wondering if you are including Chlorarachnion (Chlorarachniophyceae etc.) in the list under algae or elsewhere (it's a green zooflagellate treated under the botanical Code) - did not see it - here is the treatment from AlgaeBase: http://www.algaebase.org/search/species/detail/?species_id=59340. It is currently missing in CoL because previously supplied by AlgaeBase.<br /><br />Hope the above is helpful,<br /><br />Regards - TonyAnonymoushttps://www.blogger.com/profile/00938884035250546549noreply@blogger.comtag:blogger.com,1999:blog-2326624813533383062.post-90580622750827174222016-04-13T19:55:44.767+02:002016-04-13T19:55:44.767+02:00For these examples the Plant list is a better sour...For these examples the Plant list is a better source, but of course this is a very small sample. It's frustrating that you can't get deeper into the Synonymic Checklists of the Vascular Plants to find out how they reached their conclusion. The fact it has O. stricta as a synonym doesn't build confidence. However, this is not really a reflection on the GBIF backbone.Anonymoushttps://www.blogger.com/profile/01823490603450519912noreply@blogger.comtag:blogger.com,1999:blog-2326624813533383062.post-84455478172703440212016-04-13T16:54:10.622+02:002016-04-13T16:54:10.622+02:00Oxalis acetosella is another improved example. We ...Oxalis acetosella is another improved example. We only had "Oxalis acetosella auct. non L." treated as a synonym for O. montanum which all the GBIF occurrences of O. acetosella were matched to: http://www.gbif.org/species/2891761<br />This was clearly wrong, e.g. this record: http://www.gbif.org/occurrence/1236911939/verbatim<br /><br />Now we correctly have Oxalis acetosella L. in the backbone http://www.gbif-uat.org/species/8235501 and that above record is linked to it: http://www.gbif-uat.org/occurrence/1236911939/verbatimAnonymoushttps://www.blogger.com/profile/02525336976753861766noreply@blogger.comtag:blogger.com,1999:blog-2326624813533383062.post-43132532268236367892016-04-13T16:40:03.923+02:002016-04-13T16:40:03.923+02:00Thanks Quentin. The variety synonyms are indeed sy...Thanks Quentin. The variety synonyms are indeed synonyms because the source taxonomies refer to them as synonyms. In the case of Oxalis corniculata var. atropurpurea it is ITIS: http://www.gbif-uat.org/species/102292804<br /><br />Oxalis stricta is treated as a synonym by the Catalogue of Life which again refers to World Plants: Synonymic Checklists of the Vascular Plants of the World: http://www.gbif-uat.org/species/116689209<br /><br />Would you think plants are treated better in a different source such as The Plant List?<br />http://www.theplantlist.org/tpl1.1/record/kew-2394269Anonymoushttps://www.blogger.com/profile/02525336976753861766noreply@blogger.comtag:blogger.com,1999:blog-2326624813533383062.post-16519262451237232762016-04-13T14:18:15.998+02:002016-04-13T14:18:15.998+02:00Thanks Peter. H. hispanica is available in the bac...Thanks Peter. H. hispanica is available in the backbone: http://api.gbif-uat.org/v1/species/match?name=Hyacinthoides%20hispanica&kingdom=plantae<br /><br />If you are aware of blockers please let us know!Anonymoushttps://www.blogger.com/profile/02525336976753861766noreply@blogger.comtag:blogger.com,1999:blog-2326624813533383062.post-63726320700813212842016-04-13T12:14:36.078+02:002016-04-13T12:14:36.078+02:00Can't wait for the new backbone to come online...Can't wait for the new backbone to come online, as we have been using the name match service intensively the last couple of weeks to be able to merge taxa from different sources on their gbif acceptedKey. Hyacinthoides hispanica is one of the taxa that is currently an issue for us.Anonymoushttps://www.blogger.com/profile/18072937114922733628noreply@blogger.comtag:blogger.com,1999:blog-2326624813533383062.post-38754172131929728322016-04-13T07:27:28.662+02:002016-04-13T07:27:28.662+02:00I had a look at the genus Oxalis, because it is on...I had a look at the genus Oxalis, because it is one of the few that I know a little about. Two things struck me, firstly, varieties are often given synonym rank, the example I spotted was Oxalis corniculata var atropurpurea. This is a widely accepted variety, so this surprised me. Secondly, Oxalis stricta is listed as a synonym O. dillenii. This surprised me because although there have been many name changes of these two species O. dillenii was described after O. stricta so the name O. stricta would always have priority. I imagine these issues come from the sources databases, rather than the way you constructed the backbone. The problems seem to stem from the Synonymic Checklists of the Vascular Plants of the World, but I could not dig any deeper to find out how these names got to where they are.<br />Anonymoushttps://www.blogger.com/profile/01823490603450519912noreply@blogger.comtag:blogger.com,1999:blog-2326624813533383062.post-57263734442693385452016-04-12T12:20:20.737+02:002016-04-12T12:20:20.737+02:00Thanx Markus, sounds as a good idea, I will look i...Thanx Markus, sounds as a good idea, I will look into it.Isabelhttps://www.blogger.com/profile/02908199959340993893noreply@blogger.comtag:blogger.com,1999:blog-2326624813533383062.post-27428723529532489632016-04-12T10:36:03.346+02:002016-04-12T10:36:03.346+02:00I see the occurrences don't have any extension...I see the occurrences don't have any extensions attached. In that case you could republish your entire dataset as a checklist and attach occurrences as an extensionAnonymoushttps://www.blogger.com/profile/02525336976753861766noreply@blogger.comtag:blogger.com,1999:blog-2326624813533383062.post-56525424827865325392016-04-12T10:35:52.660+02:002016-04-12T10:35:52.660+02:00Isabel, we are trying to go live with the new back...Isabel, we are trying to go live with the new backbone by the end of April. It will be a new edition of the current one in preview here, with some of the discovered bugs fixed. As I hope the post illustrates the GBIF backbone has been unchanged since 2013 and not a single new name has entered since then. But with the new one out thats changing. It still needs a tiny manual configuration change to include any new checklist as a source. <br /><br />The only dataset matching your DOI that I can see is an occurrence dataset in GBIF: http://www.gbif.org/dataset/1515ac55-d024-4ed6-9785-b90625706f59<br />We do not include names from occurrences. If you could publish that paper as a checklist with names at its heart then we can easily add you - already to the April edition if its be the end of this week :)Anonymoushttps://www.blogger.com/profile/02525336976753861766noreply@blogger.comtag:blogger.com,1999:blog-2326624813533383062.post-88352561261972517492016-04-12T10:35:10.782+02:002016-04-12T10:35:10.782+02:00You an read more about the "algae" datas...You an read more about the "algae" dataset here: https://github.com/gbif/algae<br /><br />Basically it tries to fill in the gaps of the CoL hierarchy due to the removal of Algaebase. The phyla Ochrophyta, Haptophyta & Cryptophyta for Chromista and Euglenozoa, Metamonada & Loukozoa for Protozoa.<br />Metamonada & Loukozoa are not really algae, but are another gap identified in the CoL tree which we wanted to fill.<br /><br />If you have reasons to believe we should follow a different approach or are missing key taxa please let us know. <br />It is important that any classifications fits into the current CoL tree which we need to extend and follows the spirit of their management classification described here:<br /><br />http://www.catalogueoflife.org/col/info/hierarchy<br />http://www.catalogueoflife.org/annual-checklist/2009/info_hierarchy.php<br />http://www.catalogueoflife.org/annual-checklist/2009/show_database_details.php?database_name=AlgaeBaseAnonymoushttps://www.blogger.com/profile/02525336976753861766noreply@blogger.comtag:blogger.com,1999:blog-2326624813533383062.post-75678303914701581792016-04-11T19:25:46.907+02:002016-04-11T19:25:46.907+02:00Here is a very simple dwc archive of the preview b...Here is a very simple dwc archive of the preview backbone: https://dl.dropboxusercontent.com/u/457027/nub.txt.zipAnonymoushttps://www.blogger.com/profile/02525336976753861766noreply@blogger.comtag:blogger.com,1999:blog-2326624813533383062.post-87961495346736376242016-04-11T16:59:31.681+02:002016-04-11T16:59:31.681+02:00Hello Markus
I'm interested to know why Chromi...Hello Markus<br />I'm interested to know why Chromista and Protozoa are being included as kingdoms in the algae classification. Any particular reason?Annehttps://www.blogger.com/profile/09686911131754619206noreply@blogger.comtag:blogger.com,1999:blog-2326624813533383062.post-90124818939826906482016-04-11T13:58:01.933+02:002016-04-11T13:58:01.933+02:00Thanks Tony, we use your latest IRMNG export and h...Thanks Tony, we use your latest IRMNG export and have included all the genera. So that should help a lot to fill the algae gap together with the higher replacement classification I did. I haven't verified yet how well the IRMNG genera actually fit into that classification, should be interesting.<br /><br />The IRMNG homonym list we don't use in this algorithm anymore, so there is no need to treat that special. Said that the well curated list of genera (embedded in the regular, full IRMNG) is of very high value still for us. Most importantly it would be great if VLIZ would be able to automatically generate a new dwc archive on a regular basis or just when changes had been incorporated if that is rather rare. Maybe even using the IPT which they make heavy use of already: http://ipt.vliz.be/Anonymoushttps://www.blogger.com/profile/02525336976753861766noreply@blogger.comtag:blogger.com,1999:blog-2326624813533383062.post-34047671326139074842016-04-11T12:04:39.201+02:002016-04-11T12:04:39.201+02:00Looking very much forward to the launch of the new...Looking very much forward to the launch of the new backbone. Do you have a timeframe? (though probably difficult to say with the blockers you mention). What I really wanted to know is whether inclusion of new names lists is on halt currently? E.g. Denmark for a while has had a dataset with new row-beetle names (http://doi.org/10.11646/zootaxa.3893.1.2) sitting on GBIF, still without the names being recognised :-) What do you recommend we do?Isabelhttps://www.blogger.com/profile/02908199959340993893noreply@blogger.comtag:blogger.com,1999:blog-2326624813533383062.post-36022107262045680342016-04-07T01:27:39.011+02:002016-04-07T01:27:39.011+02:00Hi Markus,
A couple of IRMNG-related comments, if...Hi Markus,<br /><br />A couple of IRMNG-related comments, if I may:...<br /><br />1. Regarding the lack of algal coverage in the present Catalogue of Life, you could get just about all the relevant genera from IRMNG (if you have not already done so), both extant and fossil, since IRMNG is pretty complete in this respect (genera supplied by Index Nominum Genericorum and other sources in the main, not AlgaeBase). Some of the family assignments may not be 100% resolved or correct, but maybe that can be addressed as a separate issue.<br /><br />2. IRMNG is presently in transition between CSIRO (location for last 10 years) and VLIZ, Belgium where it will eventually be under new editorship and direction. So if GBIF has particular needs it would be a good time to articulate them to the new custodians - for example the continuation of the IRMNG homonyms list, which I have tended to regard as a somewhat minor spinoff in the big picture of IRMNG ongoing population but would seem to be more significant to your present uses.<br /><br />Hope the above is of some interest,<br /><br />Regards - TonyAnonymoushttps://www.blogger.com/profile/00938884035250546549noreply@blogger.com