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Copy of FAQ/UKK (Copy)

Last modified by akuusija@helsinki_fi on 2024/02/12 14:24

Getting access to Kotka, logging in

  1. I have forgotten my password or for some other reason I cannot login to Kotka. Help?
    • Please contact kotka(at)luomus.fi and explain the situation.
  2. A new staff member needs access to Kotka, what should I do?

Specimens, data entry and edit

  1. What is wrong with the import, when in the preview I get an error message saying value is required and can't be empty but there is are no cells highlighted in red?
    • Most likely one or more mandatory columns are missing from your import file. Please make sure you have the columns MYCollectionID, MYGathering[0][MYCountry] or MYGathering[0][MYHigherGeography] and MYGathering[0][MYUnit][0][MYRecordBasis] included in your file and if importing also sample information, the column MYGathering[0][MYUnit][0][MFSample][0][MFPreparationType], too.
  2. There are some fields missing from the web form, why is this?
    • On the web forms, it is possible to choose some fields as advanced fields and show only basic fields. When editing or entering a new specimen, in the menu on the right hand side, choose "Show basic and advanced fields" to see all fields.
    • Some fields are form specific, meaning that they are used for example only for garden accession but not other types of specimens.
  3. I can't edit specimen information, why is this?
    • The owner of record for the specimen may be some other organisation than your own. If the owner information is wrong (for example a specimen in one of University of Turku's collections is owned by one of Luomus' teams but people in UTU should be able to edit it), contact either the person who entered the data, team leader of the owner organisation, or kotka(at)luomus.fi, depending on the case.
    • If you work for many organisations and need to edit all their specimen information, edit rights can be added by linking your user account to the organisations. Ask the organisation's Kotka contact person to contact Kotka support kotka(at)luomus.fi (or send a message yourself and cc the contact person).
  4. How can I delete a specimen?
    • It is possible to delete a specimen within two weeks from the date it was first created. Then delete-button is visible in edit mode on the web form If it's been more than two weeks, deletion is possible only for admins. Contact kotka(at)luomus.fi for support and give good reasons for the deletion (identifiers should be persistent). Also make sure the specimen is not connected to a transaction or the identifier has not been used in a publication, for example.
  5. How can I create specimen identifiers to another domain, for example to tun.fi when my default is id.luomus.fi?
    • In Excel import, enter the desired domain as a prefix to the namespace in MYNamespaceID, for example tun:AA.
    • Note that some namespaces can only be used in a certain domain
    • web forms:
  6. Where in Kotka do I store the vernacular name?
    • Vernacular names are not stored in Kotka, but taxonomy is handled separately in Taxon database (Copy of Handling taxonomy (Copy)).
    • If the vernacular name is written on the label or other original source, you can enter it to Taxon verbatim and use the scientific name in Taxon name.
  7. How do I delete an image from a specimen?
    • Deleting specimen images is possible for Kotka admins or users with an advanced user's role. You can ask the admins to delete images occasionally, but if you regularly work with images and often need to delete some, you can request for an advanced user's role (which does not bring any other additional rights compared to a basic user). In both cases contact kotka(at)luomus.fi

Search

  1. There seem to be some specimens missing from the search results.
    • Please check your search criteria: is there some filter that may be excluding some specimens from the search? For example edit date too tight or wrong collection? Try a collection tree search? Someone else as the editor? "Only accepted" checked?
    • Please see the following question, too.
  2. Why can't I find a specimen I just entered a moment ago?
    • Sometimes there are delays in indexing the specimen information to the search database. Normally there should only be a delay of maximum few minutes and even with some occasional problems in the indexing, the specimen information should be in Kotka search on the following day at the latest. If there are often these kind of longer delays or the problem persists, note the admins at kotka(at)luomus.fi.
    • There is most often no need to worry about the data being totally lost, the data is stored in the actual database but is just not yet indexed to the search database/engine.
    • Please remember to check your search criteria, too. For example, uncheck the checkbox "Only accepted" if the name you just entered is not the accepted name.
  3. I can't find a certain field from to search from or to have in the result table.
    • In the search, some fields may be using a different name than their label on the web from (for historical reasons). For example for Specimen location, the search field is DocumentLocation. And for Collector's ID, it is LegID.
    • You can browse all available search fields in the search settings (filter options or result options). There are also 'pseudo fields' available in search that are there just to help search information, but are not actual data fields (e.g. TaxonAndInfra)
    • Some fields from the latest addition of sample section are not yet available in specimen search (try preparation/sample search instead).

Collections, organisations, datasets

  1. An organisation is missing from the organisation list, and I need it on the specimen form. How do I add it?
    • Please double check that the organisation really is not in Kotka yet (search with different criteria in all the fields in the list of organisations). Duplicate organisations are a constant problem.
    • To add an organisation, go to the top menu, Organizations → Add organization.
    • The organisation will be available to use on the specimen web forms on the following day.
  2. How can I delete a transaction/organisation/dataset?
    • Only the admins can delete these types of resources. Contact kotka(at)luomus.fi to request for a deletion, with good reasoning (duplicates etc.)
    • Double check that the resource to be deleted is not used anywhere in Kotka, in specimens, transactions etc.
  3. I want to move a set of specimens from one collection to another, how do I do it?
    • Make a search that includes the specimens in question and export them to Excel in Kotka specific format. Change the collectionID in the Excel, save your changes to the file, and import the specimens back to Kotka. Split into a few files, if there are too many specimens for one export/import (max. 10 000 rows).

Labels

  1. Some fields are missing from Label designer, I can't add them to labels. Where do I find the fields?
    • Currently those fields that have previously been used on labels, are included in the available fields in Label designer.
    • If you require a new field to be added to use on labels, contact kotka(at)luomus.fi

Identifiers

  1. How do I get my own NamespaceID for specimens?
  2. How are specimen identifiers formed?
  3. Namespace HT: How to use it? Who uses it? What is its purpose?

Data publicity and publishing

  1. Where is the data from Kotka published? Is it in laji.fi and GBIF?
  2. When is the data from Kotka going to be in GBIF?
  3. How quickly does the data from Kotka go to laji.fi?
  4. I have specimens of sensitive species. How can I make sure that the collection locality information is not made public?
  5. I have other type of sensitive data (not sensitive species) that I need to save into Kotka but I do not want it to be public. What to do?