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EDIT Wp5 and WP6 meeting – Portal and Editor

2 July 2009, Royal Botanic Gardens, Kew

Participants: Bill Baker, Irina Brake, Ben Clark, Andreas Kolhbecker, Andreas Müller, Soraya Villalba


  • New release scheduled for the week starting 6 July.

  • Now runs in new CDM, in REST architecture, which facilitates creating new features.

  • New: Support for multiple trees. This feature allows reorganising the taxa to represent different classifications. It does not allow to have taxa switch status (accepted <--> synonym). The latter issue is difficult to solve and is not in the current work plan.

  • New: Advanced search. Allows searching by name (accepted, synonyms and/or common names), and/or by geography (TDWG levels). Results of geographic search include link to the map viewer.

  • New: Default highest rank to show in the classification tree is now configurable in the administration page.

+Improvement requested for Palmweb+: button/link for the user to show/hide the full classification (i.e. all available ranks).

  • Accounts to access the administration site should exist already but neither Irina nor Soraya could enter with their TRAC login. WP5 to look into this.

  • New: Images in search results. Row of thumbnails below the name of the corresponding taxon in search results list. Clicking on a thumbnail goes to the image tab in the taxon page. The number of thumbnails to display will be configurable in the administration page. +Discussion+: It’s a good feature to indicate the user which taxa have images, but if the results list is long it clutters the screen and makes navigation harder. This functionality is different from an image search.

+Improvements requested+:

  • Tick box to allow the user to show/hide the images in the result list.

  • Add a little icon-link that goes to the taxon page image tab if images are present.

  • Image search – IMPORTANT.

+Functionality required+:

  • Tick box in the Advanced Search to “search images” for a taxon.

  • Show result of the image search in a thumbnails grid (image gallery).

  • Under each thumbnail show a short caption and links to open the image page (i.e. viewer + metadata) or a lightbox. Caption could be the title of the image (or part of it if it’s too long).

  • Image tab in taxon page. The viewer is too small.

+Discussion+: a lightbox could be used instead of the viewer – but then zooming and panning are lost. Or, the layout could be wider – Palm group prefers the narrow layout.

+Preferred solution+: Functionality similar to that for the image results page (i.e. tab shows image gallery, thumbnails with caption and links to open image in viewer and lightbox).

  • Images in genus page.

+Functionality required+: The image tab in the genus page should show all the images for that genus. Best approach to achieve this: populate the page by searching all the images for that genus.

  • New: map viewer with zooming and panning.

+Discussion+: Agreed that this is a big improvement. But as the default map is the whole world, very small distributions are basically invisible.

+Proposed solution+: Make the TDWG names in the distribution text a link that zooms to the corresponding area in the map. Needs to be discussed with Pere.

+Other improvement required+: Include caption in the map (embedded in image) saying something like “map accurate to TDWG level distributions”. Caption should be in the image itself because the map can be downloaded/copied.

Note: Legend for status (introduced, native, etc) not needed for Diptera nor Palm portal for the moment so it will be removed in the next release. Palm group may include this kind of information in the future as it is already available in the palms checklist.

  • Sources of content in taxon page- IMPORTANT.

+Minimum functionality required+: Add a reference to a content element in a feature (this should be possible already). Better still: add multiple references for a content element (implementing this should not be too difficult). However, having multiple references for multiple elements in a feature and ordering them is apparently very complicated to implement.

  • Citations in the taxon page should be a links to the reference page and the full citation should appear when hovering with the mouse over the citation (author+year). A full list of references should be added to the print version.

  • Nomenclature reference.

+Request for Palmweb+: disable the link to the nomenclature reference and leave only the icon that opens the protologue if it is available. Currently the palm group does not have the full nomenclature references (although they might compile them in the future).

Note: The possibility to link with ViTaL to get full nomenclature reference was briefly discussed. This link could be via the Editor.

  • Further reading.

+Feature requested by palm group+. This would be a list of links that open the corresponding reference in the reference page. This could be a feature like any of the others in the taxon page, maybe similar to the Citations section in the Diptera portal. In a print version of the taxon page, the references should appear in full.

  • Bibliography page.

  • +For the Diptera+: change the format of the references: author, year, title. Further discuss this format by email.

  • +For the Palms+: remove all the references. They were imported from the checklist but they are not very useful in the context of Palmweb.

  • References import. Endnote files provided by Diptera and Palm groups. Problem to import: no mechanism to link a reference to a taxon. No conclusions about this in this meeting, needs further discussion.

  • Make portal data visible in Google

  • Add a spell checker to the search (like Google)


  • Progress towards supporting multiuser environment.

  • Next release scheduled for August 2009.

  • Support for multiple trees (as in the portals)

  • Maps are shown in “Descriptive” tab. Changes to the distribution are reflected immediately in the map.

+Desirable improvement+add areas to the distribution list by clicking directly on the map. This is done now by selecting areas from a list.

  • Images can be added to a taxon page by saving their url in the Editor’s Image tab. The images must be stored somewhere else (i.e. the Editor does not import the image to the CDM).

  • Formatting text in the descriptive elements: it’s only possible by adding HTML tags. Adding tags to the text has some risks. CATE already has mechanisms to deal with this kind of risk (e.g. data validation) that could be adopted in the Editor.

  • References can be added to a descriptive element in the “descriptive” tab in the taxon page.

  • New window to edit and manage references. This is separate from the taxon page window. Useful for de-duplication.

  • +New feature request+: mechanism to add tables to the content in a descriptive element. This may be achieved by using functionality in Eclipse, like opening an excel window to edit tables.

  • Next year, specimen data will be included in the editor.

Export functionality

Import/export from/to the Berlin model works and in the future will be done via the Editor.

Other export formats are very much needed. This and webservices should be part of next year’s work plan.

Future of the portals

It’s very likely that the Cichorieae will be supported by the BMBG at least for 5 years after the end of EDIT. The support of the Diptera portal and Palmweb is very uncertain. By the end of EDIT it should be possible to install local copies of the CDM and the content of a portal in any computer.

Ben suggested that WP5 puts forward ideas for the governance of the CDM: how further developments and maintenance of the platform could be shared by institutions that may have different priorities.

Comparison with other taxonomic websites

Agreed that the portals new to include features “typical” in a taxonomic website, such as links to specimen databases or the Genbank.

Soraya will compile and circulate a list of the “10 top” features of a web taxonomy site and a list of websites that may serve as references.


The agenda of the meeting was as follows:

1. Welcome (9:30)

  • Agenda

  • Minutes

2. Data Portals (9:40)

  • Progress on the current list of tasks

  • Discuss new bugs features (or not fully covered in tickets)

    • Images and image viewer
    • References
    • Types formatting
    • etc
  • Portal administrator

  • Data imports

  • Realistic expectations (what features will available at the end of the project, data export)

Lunch (13:00)

3. Taxonomic Editor (14:00)

  • New version

  • Geo Tools (!MapViewer, Map WebServices, ...)

  • Next meeting

End (16:45)

Updated by Andreas Müller almost 12 years ago · 25 revisions