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feature request #980

Links to relevant external website(s) in taxon pages

Added by Soraya Villalba about 11 years ago. Updated 3 months ago.

Status:
New
Priority:
Priority14
Category:
cdm-dataportal
Target version:
Start date:
10/08/2009
Due date:
% Done:

0%

Severity:
major

Description

Soraya suggested that we discuss what links we need and how they should be displayed. We think this is really important now to raise the credibility of EDIT portals. We've made a list below. In general these may be best represented by opening new windows, but if embedding is an option it would be worth considering - perhaps Andreas K etc could keep us informed if other options are available.

For us the top priority would be:

Specimen resources:

GBIF - basically open new windown to show data and maps in GBIF portal. Are there any options for embedding any of this in our pages? If so, should we be considering this? We are not sure if it would be helpful to embed or not, given that we have our own maps already.

Museum/Herbarium specimen databases (e.g. New York Botanical Garden, Missouri Botanical Garden/TROPICOS, Kew, National Herbarium of the Netherlands, NHM Paris - there are many of these and it would be useful to have the flexibility to link to any or all of GBIF, perhaps configurable under administrator options)

Molecular etc:

Genbank/NCBI - check out Solanaceae source - nicely done there, showing not just DNA sequences, but also proteins and Pubmed records.

Conservation:

IUCN - open new window in IUCN red list site.

Image resources:

  • Google Images - Open new window

  • Flickr - Open new window

  • Morphbank - Maybe? We aren't very impressed by the palm content in here. Is this important for other people?

Literature resources:

  • Google Scholar - Open in new window

  • BHL - Open in new window

Any more suggestions anyone?

Cheers,

Bill & Soraya

See Solanaceae source for an example http://www.nhm.ac.uk/research-curation/research/projects/solanaceaesource/taxonomy/description-detail.jsp?spnumber=1213


Related issues

Related to Edit - feature request #8865: more external-links to be implemented New 02/28/2020

History

#1 Updated by Andreas Kohlbecker almost 11 years ago

  • Target version deleted ()
  • Priority changed from Priority08 to Priority14

#2 Updated by Andreas Kohlbecker almost 11 years ago

Dear Soraya & Bill,

Alexander is in vacation this week. Next week we will investigate the option to embed these external resources into the data portals. If we embed there will be one question to solve. From the Dataportal we will search the external service or website by the name of the taxon and maybe also by all synonyms. The results from the external services will in many cases contain data on different taxon concepts. So there will always be a difference between the taxon concept displayed in the portal and of the embedded resultsets returned by external services.

If we would just link to GBIF, GenBank, etc we would of course avoid the burden to tackle this question.

Cheers

Andreas

#3 Updated by Andreas Kohlbecker almost 11 years ago

behalf of Bill

Yes, this is obviously an issue that concerns us all. However, just by providing a search on an accepted name and its synonyms is a wonderful thing to offer. If there is a risk that data returned by such searches is not compatible with the concepts in the portals, it might be better deliviered in a new window in the source site, rather than embedding in our site. This will be interesting to discuss when you know the options. I am looking forward to hearing more from you and we are here to help you with decision making when you need us.

All the best

Bill

#4 Updated by Andreas Kohlbecker almost 11 years ago

behlaf on Ralf

Additional resources should be:

EMBL (as an European alternative to Genbank) PubMed (another literature source)

Is it really necessary to separately link herbarium specimen databases if GBIF will be linked? Most if not all relevant collections are represented by the latter.

Another question is where all these links will be shown in the portals. It will influence layout and graphics a lot. We are a bit hesitant regarding the image resources, e.g. both Google Images and Morphbank are not really helpful for Cichoarieae.

#5 Updated by Andreas Kohlbecker almost 11 years ago

behlaf of Bill

On EMBL/Genbank - EMBL is a nucleotide database, if I understand correctly, run by EBI. EBI exchanges nucleotide data with NCBI (who host genbank) all the time, so it is really semantic to choose one over the other. NCBI, however, provide this nice cross-database search called Entrez http://www.ncbi.nlm.nih.gov/sites/gquery which delivers results on nucleotides, proteins, PubMed, etc etc etc. I think we are primarily interested in the nucleotide and literature results, I guess, but it would be great to use that mechanism for the breadth of the resources that it explores. As I said in my last message, please look at how Solanaceae source does this - it returns results on nucleotide and PubMed embedded within the page, but if you want to see more it takes you to a full Entrez research result. I think we should emulate this.

As for herbarium specimen databases, yes I do think we need to have access to that as an option, perhaps configurable by adminstrator. Sadly, not all institutions are effectively joined up to GBIF (e.g. Kew!!!!), and many of these sites deliver images as well. I need the option to link to the catalogues of some of the most important herbaria/museums in Palmweb. I think we need it in general to be competitive.

Cheers

Bill

#6 Updated by Soraya Villalba almost 11 years ago

Hi Andreas K,

in a reply to Ralf et al. regarding their concern about linking to Google Images and Morphbank you said that the linking to external resources would be configurable and the admin will be able to switch them on/off.

What do you have in mind? A list of predifined sites shown as a dropdown list or set of checkboxes the admin can choose from?

If so, would it be possible to add more external sites to the list? The portal admin could enter the url and search string for them. That would be very useful.

Regarding presentation. The external links could appear as a box (maybe belwo the classification tree) in the taxon page entitled "Resources", ideally with labels identifying the type of resource (e.g. specimens, literature, iamges, etc). These links would open the external site in a new window.

Regarding embedding vs. linking. Even though it would be nice to extract the data from the external site, linking would be easier and probably more consistent (I guess not all sites provide a means for others to extract their data).

Soraya

#7 Updated by Andreas Kohlbecker almost 11 years ago

  • Target version changed from SPRINT PalmWebPortal 1 to SPRINT PalmWebPortal 2

#8 Updated by Andreas Kohlbecker almost 11 years ago

  • Assignee changed from Andreas Kohlbecker to Alexander Kroupa

#9 Updated by Alexander Kroupa almost 11 years ago

With Andreas K. we discussed the implementation in drupal. We would like to realize the presentation of the external links as a drupal block module. So the external links could be placed on different areas within the website.

Each link to an external website could be configured in the settings of this module. Each link could be given a name (e.g. "Search Google..."), the link to the website - except the taxon name - and the possibility to choose one link or not.

A next step could be to include synonyms into the search, if this is possible within the external webprojects.

#10 Updated by Katja Luther almost 11 years ago

  • Status changed from New to Closed
  • Resolution set to fixed
  • % Done changed from 0 to 100

#11 Updated by Gabriele Dröge over 7 years ago

  • Status changed from Closed to Feedback
  • Resolution deleted (fixed)
  • % Done changed from 100 to 0
  • Target version changed from SPRINT PalmWebPortal 2 to cdm_dataportal - Next Major Release

I would like to reopen this ticket, since the final discussion was coming up last week again and it is not fixed. Manual selection of used external services at data portal would be nice to have in settings of data portal.

Attention: link to GBIF doesn't work for infraspecific taxa! The link refers to species level. Please enable it! Example: http://dev.e-taxonomy.eu/dataportal/corvidae/cdm_dataportal/taxon/ac3e0835-6e67-4651-8c47-30b4dd35d433 currently links out to: http://data.gbif.org/species/Corvus_macrorhynchos but should link out to http://data.gbif.org/species/Corvus_macrorhynchos_intermedius instead

Thoughts about GBIF occurrence maps at cdm data portal:

would be a nice feature to embed it into the portal, since it includes all GBIF records in opposite to the specimen map at cdm data portal.

#12 Updated by Andreas Kohlbecker over 7 years ago

Replying to g.droege:

I would like to reopen this ticket, since the final discussion was coming up last week again and it is not fixed. Manual selection of used external services at data portal would be nice to have in settings of data portal.

I would rather prefer opening a new ticket.

The following links will lead you to the settings for the external links: http://dev.e-taxonomy.eu/dataportal/corvidae/#overlay=admin/config/cdm_dataportal/extlinks

Is this what you are looking for?

Attention: link to GBIF doesn't work for infraspecific taxa! The link refers to species level. Please enable it! Example: http://dev.e-taxonomy.eu/dataportal/corvidae/cdm_dataportal/taxon/ac3e0835-6e67-4651-8c47-30b4dd35d433 currently links out to: http://data.gbif.org/species/Corvus_macrorhynchos but should link out to http://data.gbif.org/species/Corvus_macrorhynchos_intermedius instead

Could you please open an new ticket for this?

#13 Updated by Andreas Kohlbecker 8 months ago

  • Tags set to external-links

#14 Updated by Andreas Kohlbecker 7 months ago

  • Target version changed from cdm_dataportal - Next Major Release to Release 5.14

#15 Updated by Andreas Kohlbecker 7 months ago

  • Description updated (diff)
  • Assignee changed from Alexander Kroupa to Andreas Kohlbecker
  • Private changed from Yes to No

#16 Updated by Andreas Kohlbecker 7 months ago

#17 Updated by Andreas Kohlbecker 6 months ago

  • Status changed from Feedback to New

#18 Updated by Andreas Müller 6 months ago

  • Target version changed from Release 5.14 to Release 5.15

#19 Updated by Andreas Müller 3 months ago

  • Target version changed from Release 5.15 to Release 5.18

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