EOL API Discussion Group

With growing interest in using the Encyclopedia of Life API (application programming interface), comes the need for an openly available place to ask and answer questions. This is the place.

The Newsfeed for this EOL Community gathers updates associated with the items belonging to its Managed Collections, including activities of its members and comments from other EOL users.

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  • Profile picture of Marie Studer who took this action.

    Marie Studer commented on "EOL Learning and Education Community":

    @Jared Lamenzo: Hi Jared! Welcome to both the EOL L+E Community and the Saguaro BioBlitz Community. Let us know if you have any questions or help using the site!

    almost 4 years ago

  • Profile picture of Roderic Page who took this action.

    Roderic Page commented on "EOL API Discussion Group":

    @Cyndy Parr: Here's an example of the EOL API not doing quite what I expect. If I search for "Wiebesia flava" using http://eol.org/api/search/1.0/Wiebesia%20flava.jsonI get this JSON:

    {"results":[{"title":"Wiebesia flava-SAG","id":12075001,"content":"Wiebesia flava-SAG","link":"http://eol.org/pages/12075001"},{"title":"Wiebesia flava Wiebes, 1993","id":852880,"content":"Wiebesia flava Wiebes, 1993","link":"http://eol.org/pages/852880"}],"totalResults":2,"self":"http://eol.org/api/search/Wiebesia%20flava.json?page=1","itemsPerPage":30,"last":"http://eol.org/api/search/Wiebesia%20flava.json?page=1","startIndex":1,"first":"http://eol.org/api/search/Wiebesia%20flava.json?page=1"}

    The first hit is "Wiebesia flava-SAG", the second is "Wiebesia flava Wiebes, 1993", which is actually what I want. I can't search using an exact match for "Wiebesia flava" because that retrieves 0 hits.

    I think what EOL is missing is an index on just canonical names, which would enable me to search for exactly "Wiebesia flava".

    almost 4 years ago • edited: almost 4 years ago

  • Profile picture of Cyndy Parr who took this action.
    Cyndy Parr removed "Rapid Response team" from the collection "The discussion collection".

    almost 4 years ago

  • Profile picture of Cyndy Parr who took this action.

    Cyndy Parr commented on "EOL API Discussion Group":

    @Roderic Page: 1. Canonical names. Ultimately, the best course may be for us to figure out a way to add this to our pages API method. For the moment, though, Nathan suggested the following:

    Genus and specific epithets fields are available in the hierarchy_entries call. For example,

    http://eol.org/api/hierarchy_entries/1.0/36023440

    To go from the search API to the canonical name requires at least three distinct API calls and some non-trivial logic to deal with cases where there are multiple results. For example,

    http://eol.org/api/search/Amanita+velosa

    then extracting the id, 6692200, (which won't always be unique, but first one should be reasonable) and calling:

    http://eol.org/api/pages/6692200

    then extracting the , 36023440, (which isn't unique, but again the first one should be reasonable) and calling:

    http://eol.org/api/hierarchy_entries/1.0/36023440

    and then extracting the dwc:genus and the dwc:specificEpithet which are buried in a list of dwc:Taxon fields.

    There are more caveats but I won't include them here, except to say that in this example we're just using Catalogue of Life hierarchy entries, and you may need to use a different hierarchy to get the canonical for other names.

    2. I've asked Rod for some examples of exact=1 searches that don't produce the results he expects. We may need to do more tweaking.

    4. As Rod knows, our GBIF and BHL processes are unlike those of our other content partners. So we'll have to make changes to expose their data. I'll make sure we discuss this with our technical team.

    And please do jump in, technical folks, if you have anything to add or change from what I've said.

    almost 4 years ago • edited: almost 4 years ago

  • Profile picture of Cyndy Parr who took this action.

    Cyndy Parr commented on "EOL API Discussion Group":

    @Tanya Dewey: I've finally gotten some responses from our technical team. I'll summarize what I've learned so far in a response to Rod.

    almost 4 years ago

  • Profile picture of Cyndy Parr who took this action.
    Cyndy Parr added "Patrick Leary" as a manager of the community "EOL API Discussion Group".

    almost 4 years ago

  • Profile picture of Katja Schulz who took this action.
    Katja Schulz joined the community "EOL API Discussion Group".

    almost 4 years ago

  • Profile picture of Tanya Dewey who took this action.

    Tanya Dewey commented on "EOL API Discussion Group":

    I was really hoping to see a follow up to Rod's comments below, esp. 1, 2, and 4. ??

    almost 4 years ago

  • Profile picture of Marie Studer who took this action.

    Marie Studer commented on "EOL Learning and Education Community":

    @Tracy Brown: Hi Tracy! Thanks for joining the EOL L+E Community! Please feel free to contact us and let us know how you are or might use EOL and we welcome your feedback. Please also check out the Discover pages (click on Discover link at the very top of an EOL page) to find out about other EOL tools, resources and activities.

    almost 4 years ago

  • Profile picture of Marie Studer who took this action.

    Marie Studer commented on "EOL Learning and Education Community":

    @jeff betz: Welcome Jeff! Glad to have you doing an internship at EOL. Looking forward to working with you.

    almost 4 years ago

  • Profile picture of Marie Studer who took this action.

    Marie Studer commented on "EOL Learning and Education Community":

    @Sibylle Noack: Hi Sibylle! Thanks for joining the EOL L+E Community! In addition to the EOL taxon or species pages, please have a look at the EOL Discover Pages (see tab at the very top of any EOL page) that have other educational resources and tools. Please also let us know how you might use EOL and if there are particular tools or resources you are looking for. We welcome all feedback.

    almost 4 years ago

  • Profile picture of Marie Studer who took this action.

    Marie Studer commented on "EOL Learning and Education Community":

    @Zhi-Shun Song: Welcome Zhi-Shun Song! Please have a look at the EOL Discover pages for other educational resources and activities. Please let us know if there are particular tools or types of resources you are looking for. We are eager to get feedback and make EOL more accessible for educational uses.

    almost 4 years ago

  • Profile picture of Valter Jacinto who took this action.

    Valter Jacinto commented on "Rapid Response team":

    Orchis anthropophora is a synonym of Aceras anthropophorum: http://eol.org/pages/1136364/overview

    almost 4 years ago

  • Profile picture of Cyndy Parr who took this action.

    Cyndy Parr commented on "Rapid Response team":

    @Valter Jacinto: That image is an individual that developed both male and female parts: a gynandromorph . We should check on Flickr to see if there are more typical images.

    almost 4 years ago

  • Profile picture of Valter Jacinto who took this action.

    Valter Jacinto commented on "Rapid Response team":

    That's not a true butterfly! http://eol.org/pages/2927031/overview

    almost 4 years ago

  • Profile picture of Kristen Lans who took this action.
    Kristen Lans removed "Mephitis mephitis (Schreber, 1776)" from the collection "The discussion collection".

    almost 4 years ago

  • Profile picture of Kristen Lans who took this action.

    Kristen Lans commented on "The discussion collection":

    @Cyndy Parr: Oops! Sometimes I am testing code on our staging server and comparing to the live eol.org site and I get my tabs mixed up. I shall remove Mr. Skunk from "The People of EOL" community!

    almost 4 years ago

  • Profile picture of Cyndy Parr who took this action.

    Cyndy Parr commented on "EOL API Discussion Group":

    Rod, taking on number 2, can you give us examples where exact=1 gives a result that is clearly not the best hit. This is something we've been working on and obviously we want to improve our algorithms. I'm checking into the canonical business.

    almost 4 years ago

  • Profile picture of Cyndy Parr who took this action.

    Cyndy Parr commented on "The discussion collection":

    @Kristen Lans: Kristen, are you saying the EOL people stink?

    almost 4 years ago

  • Profile picture of Roderic Page who took this action.

    Roderic Page commented on "EOL API Discussion Group":

    Ok, here are some things about the EOL API which drive me nuts, or which could be improved.

    1. The scientific names are not clean, they may or may not contain taxon authorities, which means my code has to clean these off if I want "canonical" names.

    2. There seems to be no relevance ordering to search results. I can't rely on the first hit being the "best" (on several occasions it is very clearly not the best hit). Even ordering by how well the name string matches the query string would help.

    3. It would be helpful to provide nice thumbnails. For my projects (e.g., http://iphylo.org/~rpage/phyloinformatics/eoliphone/ ) I've ended up grabbing the full image, centring and resizing it to create square images. An API that supports something like this would be handy.

    4. Lots of EOL content (e.g., GBIF maps, BHL references) are not exposed by the API , which means I need to query those resources myself. Why not include these?

    The EOL API has lots of potential, but has some glaring gaps. One approach to tackling these would be to try and build a version of the EOL web site using just the API. This will quickly expose the gaps.

    almost 4 years ago • edited: almost 4 years ago