Anthony Goddard

Jerome.

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  • Profile picture of Katja Schulz who took this action.

    Katja Schulz commented on "EOL API Discussion Group":

    @Colin Gerety: Thanks for the additional information. I'm still not sure what happened here, but it's clear that we need to change the way we harvest ITIS.

    about 1 month ago

  • Profile picture of Colin Gerety who took this action.

    Colin Gerety commented on "EOL API Discussion Group":

    @Katja Schulz: Just one more piece of info for when you get around to looking at the duplicate taxon problem. "Atriplex truncata" is a good example to look at. In the ITIS taxonomy hierarchy there are two taxon ids: 46189093, and 61378673. Looking at the ancestors for the two ids, there are two distinct hierarchies. The 61378673 hierarchy corresponds to the current ITIS hierarchy. The hierarchies have many entries with duplicate taxa. They finally jump back together at subkingdom Viridaeplantae. My suspicion is that ITIS may have recategorized. If you want to save historical data for any taxonomy provider there is a huge problem. If you just want current data from each provider (which I think is wise), updates should re-use all existing taxon entries an merely repatch the parent pointers.

    about 1 month ago

  • Profile picture of Katja Schulz who took this action.

    Katja Schulz commented on "EOL API Discussion Group":

    @Colin Gerety: Thanks, I think I see what you mean. I'm not sure what causes this duplication. We will have to investigate. It could be that there is a glitch that improperly generates new EOL hierarchy entries when data are reharvested from the source. It looks like this currently manifests itself only in the API and not on the site. I fear that this problem may not get fixed until EOL v3 which is scheduled for release next year.

    about 1 month ago

  • Profile picture of Colin Gerety who took this action.

    Colin Gerety commented on "EOL API Discussion Group":

    @Katja Schulz: Katja, Thank you for your quick response. The basic question is one of invariants. For the eol taxonomy to be accurate I think each unique node in the source taxonomy (in this case ITIS) should have exactly one node in the eol representation of that taxonomy. In the case I gave, there are three eol taxon entries (54403812, 46208079, and 61398808) representing a single ITIS taxonomy node (TSN 29130). That is, there are three distinct entries that share the same nameAccordingTo and sourceIdentifier. The parents are of interest only because they indicate the duplication may extend up the tree.

    about 1 month ago

  • Profile picture of Katja Schulz who took this action.

    Katja Schulz commented on "EOL API Discussion Group":

    @Colin Gerety: Hi Colin, yes multiple names from ITIS are mapped to EOL taxon 130363, but only one of the names (Geranium caespitosum TSN 29130) is accepted by ITIS. The others are considered synonyms: http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=29130#null It looks like 61398785 is the ITIS Geranium (TSN 29104), but it's not clear where 4620835 comes from. The hierarchy entry api gives an error for this value. There may be a mismapping here. They should all map to TSN 29104. We would probably have to go back to the original resource to investigate.

    about 1 month ago

  • Profile picture of Colin Gerety who took this action.

    Colin Gerety commented on "EOL API Discussion Group":

    I am using both ITIS and EOL to classify specimens. As part of this process I find an ITIS_TSN (unique name id) and map it to eol TaxonIDs and TaxonConcepts. Sometimes are multiple eol taxon trees for the same ITIS TSN. That is, a single taxon in the source taxonomy tree has multiple representations in eol. The eol page/concept 130363 has three taxon entries for the ITIS_TSN 29130. These are 54403812, 46208079, and 61398808. Each of these points to the page/concept 130363. Two of them have a parent taxon of 4620835, one has a parent of 6139875. That means there is one ITIS taxonomy tree where the species is represented twice. In the third tree the whole ITIS taxonomy is duplicated.

    about 1 month ago

  • Profile picture of Abhishek Shivkumar who took this action.

    Abhishek Shivkumar commented on "EOL API Discussion Group":

    @Yan Wong: Thanks, Would you know Jeremy Rice's email ID or any other email ID where I can clarify a couple of quick questions regarding the Pages API? Also, is there a limit on how many calls I can make with a licence with Page API per day / hour?

    2 months ago

  • Profile picture of Yan Wong who took this action.

    Yan Wong commented on "EOL API Discussion Group":

    @Abhishek Shivkumar: That's a good question. I have't tried getting deep down into the pages before. It might just be timing out, I guess. This is probably a question for Jeremy Rice

    2 months ago

  • Profile picture of Abhishek Shivkumar who took this action.

    Abhishek Shivkumar commented on "EOL API Discussion Group":

    I want to get complete details using the Page API for page id = 282. It has around 800K images ! and so I see in the Page API that I have to make a call in phases of 75 images per call (images_per_page = 75 & images_page=1.. and then again images_per_page = 75 & image_page = 2 .. and so on). I seem to not get a response back from the server after few calls (like 45 calls or something). Is there a way to get the complete json description of this page id = 282 in a single shot? Thanks Abhishek S

    2 months ago

  • Profile picture of Thomas Horn who took this action.

    Thomas Horn commented on "EOL API Discussion Group":

    Search using common names - incomplete results: When searching for the common name "birke" (English=birch) only 3 results are returned. http://eol.org/api/search/1.0.json?q=birke&page=1&exact=false&filter_by_taxon_concept_id=&filter_by_hierarchy_entry_id=&filter_by_string=&cache_ttl= (e.g. "Moor-Birke" is found as German common name of Betula pubescens) Since I would expect more results, I checked other taxa and if they have been associated with German common names. Betula pendula for example is associated with the common name "Hänge-Birke" but does not show up in the search result. http://eol.org/pages/1149364/names/common_names Why is that?

    5 months ago

  • Profile picture of Yan Wong who took this action.

    Yan Wong commented on "EOL API Discussion Group":

    @Markus Ankenbrand: It should be done already, but there was some mistake somewhere and I think it is just waiting to be deployed: https://github.com/EOL/tramea/issues/147

    9 months ago

  • Profile picture of Markus Ankenbrand who took this action.

    Markus Ankenbrand commented on "EOL API Discussion Group":

    Is it planned to add the Access-Control-Allow-Origin header to the EOL API to allow cross-origin HTTP requests? It would be really handy to create dynamic pages for organisms with content from EOL. I'm aware that I can do this with PHP on the server side but I'd prefer using AJAX on the client side.

    9 months ago

  • Profile picture of Markus Ankenbrand who took this action.

    Markus Ankenbrand commented on "EOL API Discussion Group":

    My mail address is markus.ankenbrand@uni-wuerzburg.de Many thanks again for your great help.

    about 1 year ago

  • Profile picture of Yan Wong who took this action.

    Yan Wong commented on "EOL API Discussion Group":

    @Markus Ankenbrand: Have you got an email? If you don't want to post it publicly here, send me a DM on twitter @DrYanWong

    about 1 year ago

  • Profile picture of Markus Ankenbrand who took this action.

    Markus Ankenbrand commented on "EOL API Discussion Group":

    @Yan Wong: Yes, I would appreciate that. I just had a look at the dump and I'm rather overwhelmed. Thanks in advance!

    about 1 year ago

  • Profile picture of Yan Wong who took this action.

    Yan Wong commented on "EOL API Discussion Group":

    @Markus Ankenbrand: I have some Python code for mining the dump, if you like.

    about 1 year ago

  • Profile picture of Markus Ankenbrand who took this action.

    Markus Ankenbrand commented on "EOL API Discussion Group":

    @YanWong: Hi Yan, thanks for this fast, elaborate and very helpful response. I will check out your links and add my +1. In the meanwhile I will use the wikidata JSON dump. Markus

    about 1 year ago

  • Profile picture of Yan Wong who took this action.

    Yan Wong commented on "EOL API Discussion Group":

    @Markus Ankenbrand: Hi Marcus. I had the same problem, and raised this issue about it: https://github.com/EOL/tramea/issues/40. Do comment there if it is something you would like to see - the more people ask, the more likely it is to get done (there's a big backlog of more important EoL coding improvements to make at the moment, though). The other route is to go via 3rd parties. The most promising lead here is via one of the developers at EoL, called Dima. He also runs a service called GNresolver, and I raised the issue with him there (http://globalnames.org/news/2015/09/22/otol-eol/). He is intending to do an EoL import every month or so, and eventually the IDs should be made available through a project called BioGUID (http://globalnames.org/news/2015/10/14/bishop-museum-workshop/), but I don't think that is there yet. Meanwhile, I've been using the wikidata JSON dump (https://dumps.wikimedia.org/wikidatawiki/entities/) which has booth NCBI and EOL ids for perhaps a million taxa or so. Drop me a message on my feed if you want to know more. Yan

    about 1 year ago

  • Profile picture of Markus Ankenbrand who took this action.

    Markus Ankenbrand commented on "EOL API Discussion Group":

    I want to retrieve a complete mapping from NCBI taxids to EOL page ids. I can query the API via search_by_provider but I can only ask for one taxid at a time. As I want to map more than 700,000 taxids this approach is not feasible. Is there any other way to get this kind of mapping for a large number of ids?

    about 1 year ago

  • Profile picture of tukaram who took this action.

    tukaram commented on "EOL API Discussion Group":

    I want a list of EOL plants pages with there ids for linking my site . Can it possible?

    about 1 year ago