- API-users - lists.gbif.org

Re: [API-users] DWC with "extra" images
by Matthew Cruz 04 May '22

04 May '22

Hi Matt, Yes, I did mean "multimedia.txt" and not "metadata.txt". Sorry for the confusion and thanks for seeing past it. I am very happy to learn that extra records in the extension files (media etc) are ignored and that there are no plans to change that. I was hoping for this because of the way we package our DWC file. Our occurrence data comes from our "Specify" database and pulled into the IPT server via a connection. However our multimedia/images are pulled into our "Specify" database via a feed from a separate image-server/database and then this table of data is also read by the IPT server via a connection. Under consideration is using this multimedia/image feed to populate a temporary Symbiota portal within which the occurrence data can be transcribed and entered. The occurrences will intentionally not be given a GUID since Symbiota is the source DB and rather is being used as a tool to prepare the data for import into our source DB which is "Specify". Therefore I was being faced with a question of if we were to put extra images in the "multimedia.txt" that do not have corresponding occurrence IDs yet if that would cause incorrect processing by how GBIF handles the DWC extraction. Therefore, learning that GBIF's algorithm to ignore extra records in extension files that do not match with a GUID in the "occurrence.txt" is great news! Thanks, Matthew ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 2 May 2022 17:34:13 +0200 > From: Matthew Blissett <mblissett(a)gbif.org> > To: api-users(a)lists.gbif.org > Subject: Re: [API-users] DWC with "extra" images > Message-ID: <08f90ede-83de-3305-339d-fc99b606d42c(a)gbif.org> > Content-Type: text/plain; charset="utf-8"; Format="flowed" > > Hi Matthew, > > (I think you probably mean a files like media.txt or multimedia.txt) > > In general, extra records in the extension files (media etc) are > ignored. We don't have any plans to change this. > > Cheers, > > Matt > > On 15/04/2022 17:36, Matthew Cruz wrote: > > What would happen in GBIF when processing a published DWC file if the > > metadata.txt file has an ID corresponding to an image, but that ID is > > not found in the occurrence.txt file? > > > > Does the image get ignored or published despite there being no > > corresponding metadata? > > > > What else can you tell me about this process? > > > > Thank you >

1 0

DWC with "extra" images
by Matthew Cruz 03 May '22

03 May '22

What would happen in GBIF when processing a published DWC file if the metadata.txt file has an ID corresponding to an image, but that ID is not found in the occurrence.txt file? Does the image get ignored or published despite there being no corresponding metadata? What else can you tell me about this process? Thank you

2 1

Fwd: GBIF Flagging
by Matthew Cruz 16 Apr '22

16 Apr '22

Hello, I support the team of University of Michigan Herbarium Collection Managers. They have asked me to assist them with clearing up GBIF data flagging regarding "Institution match fuzzy" and "Institution Collection Mismatch". I have two questions below in bold. I try to provide backstory along the way leading up to each question. I appreciate any help you can provide please. Here are two examples of the types of flagged data that I wish to correct. The first image is of an occurrence record from the University of Michigan [my institution]. The second image is from the New York Botanical Garden. Question 1: Is GBIF aware of a particular contributor that is currently very successful in having minimal numbers of GBIF flags on their data? If so, can you please share their name with us or a link to one of their occurrence records as we would like to pattern ourselves after them? UM Herbarium example: Reference Image 1: https://drive.google.com/file/d/1OF0j61eNGSV6S1QnLKDQlArRC3YVppc1/view?usp=… Reference Image 2: https://drive.google.com/file/d/1nlHn40adKih1WuBOW4MiKHbm-SPKX65M/view?usp=… NYBG example: Reference Image 3: https://drive.google.com/file/d/1et2cHMyB87rBB_tg0WbHqVWkXV0ycqiS/view?usp=… I have successfully cleared out the "Institution match fuzzy" by providing the InstitutionID as shown here: Reference Image 4: https://drive.google.com/file/d/1tmQAv21NTvrs0XZRKK8O5VJ9OZNmGo63/view?usp=… Next what I found is that our database is sending "Subcollection" values such as "Algae", "Fungi", etc as the value that gets mapped to "CollectionCode". You can see in the example above, it indicates "Fungi" was received. The problem with this is that the collection code is actually "MICH" as indicated on this page: https://www.gbif.org/grscicoll/collection/62289b33-ae4f-438c-8574-bd27b348c… We want to keep our IPT feed as it is and report these subcollection values instead of "MICH". I found that there is this page that lists a property called "Alternative Codes". Below is a screenshot: Reference Image 5: https://drive.google.com/file/d/1jqylXC5J7ya3NHMNk7Zee5ANLs24lvqi/view?usp=… If I click the "Suggest" button, then the following form is rendered: Reference Image 6: https://drive.google.com/file/d/1HGAQSSrgnL08yn88vFr65REIF4cNfsIq/view?usp=… Reference Image 7: https://drive.google.com/file/d/1gRlvnzJcujWA_cK9Izwg6Y8vsvV9oEWb/view?usp=… The tooltip is promising so I tried to find documentation on this but could not. Question #2: a. How is this "Alternative Codes" supposed to be used? b. Is there documentation on this? c. If I populate this form with the subcollection values: "Algae", "Fungi", etc, will it enable a match? Here are two API calls, one with the correct code, "MICH" and one with the subcollection code that is passed in via IPT: "Algae": FUZZY: https://api.gbif.org/v1/grscicoll/lookup?institutionCode=MICH&institutionId… VS EXACT: https://api.gbif.org/v1/grscicoll/lookup?institutionCode=MICH&institutionId… d. After submitting this form, what happens? Who reviews it? How is it approved? How long does approval take? Thanks for your time and consideration. Sincerely, Matthew

1 0

Taraxacum of Europe
by Sylvain Ard 12 Apr '22

12 Apr '22

Hello, I want to do an API request to get the list of all species of Taraxacum genus of Europe sorted by country please. Thank you Kind regards Sylvain Ard 0549507724 0778380991 sylvain.ard(a)gmail.com http://sylvain-ard.fr Entreprise individuelle SIRET : 80079243400022 Appt 26 Bât A Résidence Le Patio 83 rue de la Bugellerie 86000 Poitiers

2 1

import all images of all occurences of a taxon
by Sylvain Ard 08 Apr '22

08 Apr '22

Hello, I want to import all images of all occurences of french Taraxacum. I wrote the PHP file joined which lists the Taraxacum species from Taxref 15 then list nubKeys then lists occurences and download images of all occurences of all species. But in the web version of GBIF I can see that I don't get all images. Thank you for help Best regards Sylvain Ard 0549507724 0778380991 sylvain.ard(a)gmail.com http://sylvain-ard.fr Entreprise individuelle SIRET : 80079243400022 Appt 26 Bât A Résidence Le Patio 83 rue de la Bugellerie 86000 Poitiers

1 3

/species/suggest - higherClassificationMap question
by Szlamka József 12 Mar '22

12 Mar '22

Hi API gurus, I assume, the search box functionality in the species page of gbif homepage (e.g.: https://www.gbif.org/species/5298708) is based on "suggest". There each result contains the scientific name and the full taxonomic hierarchy e.g. "Iris pumila subsp. attica (Boiss. & Heldr.) K.Richt. Subspecies | Plantae > Tracheophyta > Liliopsida > Asparagales > Iridaceae > Iris > Iris pumila". My question: how is the hierarchy implemented? Is it based on "higherClassificationMap"? How? When I play with the suggest api, the XMLHttpRequest responseText in raw text format contains the taxonomic hierarchy correctly (i.e. the physical order of the entries in "higherClassificationMap" is correct). Unfortunately after JSON.parse the resulting javascript object does not hold any information about the physical order of the key/value pairs. Is there any smart way to overcome this, or shall I hardcode the hierarchy manually? Thanks in advance. József Szlamka

2 2

recordedByID, identifiedByID, IPTs, and API
by Shorthouse, David 29 Jan '22

29 Jan '22

Folks, I note this new change: **************** 3) The terms Recorded By ID, Identified By ID and Subgenus are now part of Darwin Core, and move from a GBIF namespace to the TDWG namespace. (The change is visible in meta.xml files of Darwin Core Archive downloads, and on verbatim occurrence records.) **************** What happens if a data provider has either not updated the core/extensions in their IPT or are producing a DwC-A on their own? If their meta.xml continues to use the GBIF namespace for what will soon be a DwC namespace for their mapped recordedByID or identifiedByID terms, will the content in these be silently ignored when processed at GBIF's end? If this is the case, does GBIF have a mechanism to fan out communications to all affected data providers such that they can immediately update their IPTs &/or adjust how their meta.xml files are produced & then republish their datasets? Thanks, David Shorthouse

3 3

Update of GBIF occurrence index to latest Darwin Core standard
by Matthew Blissett 29 Jan '22

29 Jan '22

Dear API users, Next week we will update the GBIF.org occurrence index, API and website to align with updates to the Darwin Core standard released last year. Two changes deserve attention, as they may need minor changes to existing code, scripts, queries etc: 1) A new basis of record, Material Citation, replaces the obsolete Literature basis of record. Literature was removed from Darwin Core some years ago, but GBIF's index retained the term since existing datasets were using it. These records will now appear as Material Citations, which has a broader definition: https://dwc.tdwg.org/list/#dwc_MaterialCitation Additionally, the "Unknown" basis of record will no longer be used, instead records will be shown with an "Occurrence" basis of record. 2) The existing term Establishment Means now has an official vocabulary in Darwin Core. The old GBIF enumeration will no longer be used, and values of this term will instead be matched to an element of the new vocabulary. See https://dwc.tdwg.org/list/#dwc_establishmentMeans for the term definition and https://dwc.tdwg.org/em/ for the new vocabulary. GBIF's vocabulary used for interpretation (containing synonyms etc) is here: https://registry.gbif.org/vocabulary/EstablishmentMeans 3) The terms Recorded By ID, Identified By ID and Subgenus are now part of Darwin Core, and move from a GBIF namespace to the TDWG namespace. (The change is visible in meta.xml files of Darwin Core Archive downloads, and on verbatim occurrence records.) Other changes include: 4) The new terms Degree of Establishment and Pathway are also supported, in the same way as Establishment Means. https://dwc.tdwg.org/list/#dwc_degreeOfEstablishment / https://dwc.tdwg.org/doe/ / https://registry.gbif.org/vocabulary/DegreeOfEstablishment https://dwc.tdwg.org/list/#dwc_pathway / https://dwc.tdwg.org/pw/ / https://registry.gbif.org/vocabulary/Pathway 5) New/additional terms including Vertical Datum, Verbatim Identification, Subfamily, Infrageneric Epithet and Cultivar Epithet will be shown on occurrences. Note these are not yet interpreted — interpreting the taxonomic terms will require support from the GBIF Backbone Taxonomy and Checklistbank. The IPT's schemas will also be updated to allow publication of datasets using these changed or updated terms. We will write to the IPT mailing list with further details on this. Best regards, Matt Blissett

1 0

Re: [API-users] Welcomed to the "API-users" mailing list (Digest mode) , User Administrator Log In Request
by Olongo Shomba 17 Jun '21

17 Jun '21

I Hereby Affirm The Present Proceedings And Request That You Email To Me The E-Link Without reCaptcha Nor Mailchimp Nor Coockies Blockers To Register To Users Administrator List And As Permanent Unique Administrator Of All Accounts Services Entreprises Researches Academies Interactivities Infrastructures Structures Estates Laboratories Supermarkets Offices Properties Equipings Remittances Transcripts Publishings Concessions Hotels Etc , Email This Inserated Visible Clickable Loginable To The Present Request Reception Acknowledgement Email Message As Fast As You Can , Addressed Particularly To Unique Myself DR.MR.OLONGO SHOMBA PAUPAUL YUSSEF OL-SHO MELCHISEDEK, On 6/17/21, api-users-request(a)lists.gbif.org <api-users-request(a)lists.gbif.org> wrote: > Welcome to the API-users(a)lists.gbif.org mailing list! > > To post to this list, send your message to: > > api-users(a)lists.gbif.org > > General information about the mailing list is at: > > https://lists.gbif.org/mailman/listinfo/api-users > > If you ever want to unsubscribe or change your options (eg, switch to > or from digest mode, change your password, etc.), visit your > subscription page at: > > https://lists.gbif.org/mailman/options/api-users/mospaupol%40gmail.com > > > You can also make such adjustments via email by sending a message to: > > API-users-request(a)lists.gbif.org > > with the word `help' in the subject or body (don't include the > quotes), and you will get back a message with instructions. > > You must know your password to change your options (including changing > the password, itself) or to unsubscribe without confirmation. It is: > > Newaccount2. > > Normally, Mailman will remind you of your lists.gbif.org mailing list > passwords once every month, although you can disable this if you > prefer. This reminder will also include instructions on how to > unsubscribe or change your account options. There is also a button on > your options page that will email your current password to you. > -- Mr. OLONGO-SHOMBA Paupol

1 0

Download ZIP-File via VBA
by Reetz, Michael (NLPV) 18 May '21

18 May '21

Hello, I'm trying to query and download occurences with some subs written in VBA. While querying works fine, download leads to errors. At the end oft he query, I have a download link for a ZIP-archive. Putting this into a browser address field lets me download the archive. Giving it to a VBA-Object returns errors. E.g., Set http = CreateObject("WinHttp.WinHttpRequest.5.1") strURL_Request = "https://api.gbif.org/v1/occurrence/download/" & strDownload http.setTimeouts 30000, 30000, 30000, 30000 http.Open "GET", strURL_Request, False http.send returns a jason file that contains the download link. I extract this link and use it as parameter in the next step: http.Open "GET", strURL_ZIP, False http.send This results in a timeout. Using "Microsoft.XMLHTTP" alternativly returns "Access denied" Is this a problem with our network restrictions or does the GBIF server block the query? Kind regards Michael Mit freundlichen Grüßen Im Auftrag Michael Reetz ***************************************** Nationalpark-Verwaltung Niedersächsisches Wattenmeer Virchowstr. 1 26382 Wilhelmshaven Tel.: +49 (0) 4421 911 291 Fax.: +49 (0) 441 799 61039 e-mail: michael.reetz(a)nlpv-wattenmeer.niedersachsen.de<mailto:michael.reetz@nlpv-wattenmeer.niedersachsen.de> Web: http://www.<http://www.nationalpark-wattenmeer.niedersachsen.de/>nationalpark-wattenmeer.de Flussgebietsmanagement Übergangs-/Küstengewässer NLWKN * Betriebsstelle Brake / Oldenburg e-mail: michael.reetz(a)nlwkn.niedersachsen.de<mailto:michael.reetz@nlwkn.niedersachsen.de> Web: http://www.nlwkn.niedersachsen.de<http://www.nlwkn.niedersachsen.de/>

2 3