Roderic PageAdminRoderic Page (Admin, biostor)

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      1 comment  ·  General  ·  Admin →
      Roderic PageAdminRoderic Page (Admin, biostor) commented  · 

      The simplest way is to use the Disqus widget at the bottom of the page to leave a comment. Any comments are emailed to me, so I will then be able fix the issue.

    • 16 votes
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        planned  ·  8 comments  ·  General  ·  Admin →
        Roderic PageAdminRoderic Page (Admin, biostor) commented  · 

        If you tell me the links to the articles I'll take a look at them and see if I can fix them.

        Roderic PageAdminRoderic Page (Admin, biostor) commented  · 

        BioStor only has articles whose pages have been scanned by BHL. The article you are after has not been scanned by BHL, but you can get a copy here: http://dx.doi.org/10.1080/00222933008673104

        Roderic PageAdminRoderic Page (Admin, biostor) commented  · 

        I'm working on a graphical tool to easily add missing pages. Meantime, I need to add them manually. BioStor works by finding page ranges that match bibliographic citations, and these typically do not include the plates.

        Roderic PageAdminRoderic Page (Admin, biostor) shared this idea  · 
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          2 comments  ·  General  ·  Admin →
          Roderic PageAdminRoderic Page (Admin, biostor) commented  · 

          Thanks for reminding me about this example. I've fixed it, and the paper you mentioned (http://biostor.org/reference/53815). Locating pages in BHL is sometimes tricky, and my code sometimes matches caption numbers rather than page numbers (especially if the page numbers aren't simple). Another problem (which affected the Proceedings of the Linnean Society of New South Wales article) is that BHL can change the pagination of a scanned item, which sometimes means the pagination in BHL and BioStor can get out of sync. It's little thing like this which make the mapping less than trivial.

          Roderic PageAdminRoderic Page (Admin, biostor) shared this idea  · 
        • 1 vote
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            3 comments  ·  General  ·  Admin →
            Roderic PageAdminRoderic Page (Admin, biostor) commented  · 

            Good suggestion. Do you mean lats and longs for individual papers, the map view, the whole database? Are there other formats (e.g., KML) that might also be of use?

          • 5 votes
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              planned  ·  5 comments  ·  General  ·  Admin →
              Roderic PageAdminRoderic Page (Admin, biostor) commented  · 

              @timrobertson100 Thanks for the tip on smallint and MyISAM.

              I've used nested sets in other projects. Can't recall why I didn't for this one, possibly because I needed paths for the tree display of CoL names found in a reference, and just reused that code.

              Roderic PageAdminRoderic Page (Admin, biostor) commented  · 

              @timrobertson100 I'm using a path string as the index, rather than nested sets. Haven't checked whether nested sets would be faster.

              Can you expand on "(I have done a lot of large tables and the effect of using the smallest numeric type possible is very significant for these kind of tables)"? Do you mean that the index should be the smallest integer field possible?

              Roderic PageAdminRoderic Page (Admin, biostor) commented  · 

              Good idea. I'd thought of having thumbnails of the references in the treemap (using, for example, a quantum treemap http://dx.doi.org/10.1145/571647.571649 ). I'll explore this idea further.

            • 2 votes
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                1 comment  ·  General  ·  Admin →
                Roderic PageAdminRoderic Page (Admin, biostor) commented  · 

                The hierarchy is, but it only allows you to go back up the classification. For example, if you've reached "Arthropoda" and want to go back to "Animalia", just click on "Animalia." Did you have something else in mind?

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                  9 comments  ·  General  ·  Admin →
                  Roderic PageAdminRoderic Page (Admin, biostor) commented  · 

                  @jim_croft Donat Agosti et al. have done some work on recognising taxonomic descriptions, see also http://dx.doi.org/10.1002/asi.20463. I suspect, given page numbers (e.g., from IPNI in the case of plants) we could do a pretty good job of automatically extracting the descriptions from BHL

                  Roderic PageAdminRoderic Page (Admin, biostor) commented  · 

                  @jim_croft The wiki example was manually constructed, but this could be done automatically at page level. If we knew what page the description occurred on, that page could be automatically transcluded into the taxon page. In the Rana bolyii example I transcluded just the description. These are harder to find automatically, so maybe a first pass would be to transclude pages, then have users refine that if they wished.

                  Transclusion http://en.wikipedia.org/wiki/Transclusion is another phrase coined by Ted Nelson http://en.wikipedia.org/wiki/Ted_Nelson, who also coined hypertext and hypermedia.

                  Roderic PageAdminRoderic Page (Admin, biostor) commented  · 

                  @emeyke A parent field is one option (and this model could be extended to include articles [parent=journal] and book chapters[parent=book], although at present those links are made via identifiers [articles with same issn belong in same journal]).

                  However, for articles that are continuations there isn't necessarily a parent, it's more a linear chain of articles (i.e., it's a list not a tree).

                  Roderic PageAdminRoderic Page (Admin, biostor) commented  · 

                  @jim_croft Partly I'm trying to make my life simpler, which means on occasion not trying to replicate how biologists may treat an article, but handling the article in a way that makes it easier for me. This means treating continuations as separate articles, each individually addressable (i.e., they each have their own URL). To me this makes sense as people can (and do) cite these separately, plus there may be reasons to be able to refer to them separately (e.g., date of publication will vary across the articles). I guess there are many ways to aggregate things (pages into articles, articles into journals, articles into a series of articles, etc.), and ideally each "unit" will be addressable. Hence, one could imagine creating an aggregation of the four articles in the example that started this thread (or, indeed, the two article aggregation with the title "Further gleanings in British Conchology").

                  Regarding extracting bits from within a reference, this is what I'm exploring with the wiki. For example, http://biostor.org/wiki/Rana_boylii contains a page fragment from http://biostor.org/wiki/Page:Proceedingsofaca07acad.djvu/84, which contains the original description of this frog. I guess this is what you're after?

                  Given the effort involved, it's likely that the wiki will be the best place to create and explore links between names, publications, and fragments of publications, such as descriptions, figures, maps.

                  Roderic PageAdminRoderic Page (Admin, biostor) commented  · 

                  I guess my preference is to treat these as separate articles as it keeps the data model simpler (pagination for each reference is bounded by a start and end page), plus it enables people to cite individual parts if they wish. One approach would be to add a field linking the parts together (i.e., "is continuation of") so users could discover the links between the parts.

                  The example of Jeffreys, J. G. (1859). "Further gleanings in British Conchology." Annals and Magazine of Natural History (3)3: 30-43, 106-120 is interesting. I've added both parts to BioStor (http://biostor.org/reference/50267 and http://biostor.org/reference/50268). The first part (see http://www.biodiversitylibrary.org/page/22070184 ) states "[Continued from vol. ii. p. 133.] ", which corresponds to http://biostor.org/reference/50269, which itself is a continuation of http://biostor.org/reference/50270. These four articles span three volumes -1,2, and 3 of series 3, and have two titles "Gleanings in British Chonchology" and "Further Gleanings in British Chonchology".

                  My own view is that trying to replicate some of the more intricate practices of citation in the taxonomic literature is probably a mistake. That said, it might be worthwhile deveoping parses to handle strings like "Jeffreys, J. G. (1859). "Further gleanings in British Conchology." Annals and Magazine of Natural History (3)3: 30-43, 106-120" and return the set of articles this corresponds to.

                • 3 votes
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                    under review  ·  3 comments  ·  General  ·  Admin →
                    Roderic PageAdminRoderic Page (Admin, biostor) commented  · 

                    Much of this functionality exists, but I haven't made it publicly accessible. BioStor can import RIS files and search for best hits, and indeed this is how I've created much of the content to date. I guess you'd like an interface where you could upload such a file and see the results?

                  • 2 votes
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                      planned  ·  1 comment  ·  General  ·  Admin →
                      Roderic PageAdminRoderic Page (Admin, biostor) commented  · 

                      This is the same request as http://biostor.uservoice.com/forums/36526-general/suggestions/428913-support-plates. Probably the best way to handle plates is via the wiki being developed to edit pages. For each article we could specify a set of pages that corresponds to the article, and this set could be discontinuous (i.e., include plates at end of volume)

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                        0 comments  ·  General  ·  Admin →

                        I’m planning to do something like this. Initially I’ll look at extracting specimen codes (which include museum codes), mainly because I’m interested in citation of museum specimens, but also because if the specimens are georeferenced we can then georeference taxa and publications about those taxa.

                        Roderic PageAdminRoderic Page (Admin, biostor) supported this idea  · 
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                          0 comments  ·  General  ·  Admin →

                          First attempt to deal with this adds check that ending page (epage) and issue (“issue”) in database match OpenURL query. If OpenURL string has issue, and this matches the one in the database then we accept the match. If ending pages match, we check that titles have > 90% match (if OpenURL atitle field is set).

                          Roderic PageAdminRoderic Page (Admin, biostor) shared this idea  · 
                        • 3 votes
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                            under review  ·  1 comment  ·  General  ·  Admin →
                            Roderic PageAdminRoderic Page (Admin, biostor) commented  · 

                            The obvious question is which journals to target first? I'm tempted to go after Zootaxa and Zookeys, plus some Brazilian journals that are Open Access and have XML available (e.g., http://dx.doi.org/10.1590/S0034-71081998000400013 ).

                            Roderic PageAdminRoderic Page (Admin, biostor) shared this idea  · 
                          • 2 votes
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                              planned  ·  0 comments  ·  General  ·  Admin →
                              Roderic PageAdminRoderic Page (Admin, biostor) shared this idea  · 
                            • 1 vote
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                                0 comments  ·  General  ·  Admin →
                                Roderic PageAdminRoderic Page (Admin, biostor) shared this idea  · 
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                                  0 comments  ·  General  ·  Admin →
                                  Roderic PageAdminRoderic Page (Admin, biostor) shared this idea  · 
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                                    0 comments  ·  General  ·  Admin →
                                    Roderic PageAdminRoderic Page (Admin, biostor) shared this idea  · 
                                  • 1 vote
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                                      started  ·  0 comments  ·  General  ·  Admin →
                                      Roderic PageAdminRoderic Page (Admin, biostor) shared this idea  · 
                                    • 5 votes
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                                        0 comments  ·  General  ·  Admin →

                                        Yes, absolutely need something like this. For now I just open the image in a new window if I need to look at it. One option would be a lightbox-style approach (I already use this to look at Reference Finder search results). I do like the idea of keeping the image within the bounds of the current viewer.

                                        Roderic PageAdminRoderic Page (Admin, biostor) supported this idea  · 
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                                          under review  ·  1 comment  ·  General  ·  Admin →
                                          Roderic PageAdminRoderic Page (Admin, biostor) commented  · 

                                          I assume you mean login to UserVoice? I tested it with my Yahoo account (just my user name, not my full Yahoo email address) and it worked fine. Can you try again?

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