Online resources for palaeontologists

I was chatting to Mike Taylor the other day about Cladestore as I couldn’t find the page I needed and was surprised he didn’t know of it. To be fair it did start off well and then rather sank, but the principle is sound and it seemed relevant enough that he might know of it. It is, in short, an archive for the various files and datasets used for phylogenetic analyses. Obviously these are generally published alongside any paper that they feature in, but typing these out again or taking the raw data and formatting it into a useable manner can be a pain, and it’s not always easy to get things out of the original authors. The idea therefore was to create and archive for these files so they were easily accessible to all. Since this does seem little known, it’s well worth advertising. And I should add that despite it’s slight antiquity, I believe they still take submissions so send ‘em your nexus and tre files.

Coupled with my reference to the Paleobiology Database earlier and it got me thinking. It would be nice if there was a single, simple, one-stop-shop for all manner of palaeo websites and online resources that are useful to researchers and those interested in the field. So I’ll try and create one, as it’ll help me learn and I expect, help my colleagues. So, anything you can think of, do submit it below. I’m thinking general stuff – a database of tyrannosaur specimens, or pterosaur papers is fine but it won’t be of much use to too many people so it’s not really worth putting here. I’m thinking of major resources that cover whole fields or are simply so vast with the data collection that they are must-know-abouts.

Here’s the few I can think of, add yours below and I’ll package them all up. And do spread the word please – blog and tweet this. This could, I think be very useful to a lot of people.

VertNet – online registry of vertebrae specimens (recent and fossil)

iDigBio – index of specimens in museums (often with photos)

Cladestore – archived phylogenetic datasets

Morphobank – more phylogentic datasets

FigTree – creates phylogeny diagrams for publication

Palaeobiology Database – data of fossil specimens, deep and wide set of data

Tree of life – phylogenetic tree of the whole diversity of life

Palaeotology Journals – Jerry Harris’ lists of journals, major and minor, that publish palaeo papers

Rankings of Palaeo Journals – Kenneth de Baets’ list of journals and things like IF, SJR, OA etc.

Polyglot Paleontologist – translations of non-English papers

The Marsh Archive – PDFs of papers by Marsh – archive of stratigraphic data

Phylogeny programs – list of phylogenetics software

Morphometrics – various resources for morphometric analyses

Morphobank -hmm, link doesn’t load for me…

Digimorph – digital anatomy archive of extant and extinct taxa

Comparative osteology database – mostly mammals and a few birds, but very good

3D skulls – Witmer Lab visualisations and scans of various taxa extant and extinct

Paleoportal – search museum collections for specimens

Data Dryad – data of all kinds from published papers

Figshare – data of all kinds from unpublished studies.

Biomesh – FEA models and properties.

Biodiversity library – huge archive of books and paper.

Microstrat – stratigraphy database

I’ve started adding these as the comments come in so it’s easier for people to see and avoid duplicates rather than have to hunt through the comments to see if they have been suggested or not.

20 Responses to “Online resources for palaeontologists”

  1. 1 protohedgehog 09/02/2012 at 2:05 pm – List of phylogenetic software. – List of papers with cladistic matrices including Mesozoic dinosaurs, including nexus files for some (in progress) – Everything you’ll ever need for morphometrics – For images

    Just a few, hope they help!

    • 2 David Hone 09/02/2012 at 2:15 pm

      Yes great stuff thanks! I’d forgotton about the Washinton one for sodtware, used to have that bookmarked on my old machine and had forgotten! Most welcome to be reminded of it.

      And disappointed with myself for not knowing Graeme’s collection!

      Thanks for this and the tweet.

  2. 3 fernanda castano (@ferwen) 09/02/2012 at 2:14 pm

    Ameghiniana is a quarterly journal that publishes original contributions on all aspects of the paleontology. It’s the main palaeontological publication in Latin America.
    AMEGHINIANA on line

  3. 4 fernanda castano (@ferwen) 09/02/2012 at 2:27 pm

    The Digital Morphology library

    Witmer’s Lab where they specialize in high-resolution cranial anatomy

  4. 5 Andy Farke 09/02/2012 at 2:28 pm

    PaleoPortal Collections Search – tool for searching many North American museum collections simultaneously

  5. 6 Ross Mounce (@rmounce) 09/02/2012 at 2:32 pm – collected some data that isn’t enough for a paper? Don’t have time to write it up? Want somewhere to archive your previously published data for free, to make it available for others to use and cite?

    any kind of data accepted: spreadsheets, nexus data, images, figures…

    it’s not particularly aimed at paleontology, but nor does it exclude it, thus it’s well worth consideration. a data store strictly (I believe) for publication-related data. Definitely to be recommended. Certain big journals e.g. Evolution already mandate Dryad data deposits for their publications
    it’s the way I think all serious research journals should go tbh – transparent, re-usable data, provided in sensible formats (e.g. not pdf’d) for more verifiable and repeatable research (higher standards).

  6. 7 David Hone 09/02/2012 at 2:45 pm

    This is great stuff coming in, thanks all. More please! 🙂

  7. 8 Eric Snively 09/02/2012 at 2:57 pm archives finite element models and material properties.

  8. 9 Henrique Niza 09/02/2012 at 3:59 pm – theropod related articles collected in PDF format. – ankylosaur related articles collected in PDF format. (It is temporarily unavailable I believe)

  9. 10 Andy Farke 09/02/2012 at 4:05 pm

    Aves 3D Database – surface scans of many bird bones

    • 11 David Hone 09/02/2012 at 4:10 pm

      I know of this through leon of course but thought it might be a bit specific. Not that birds are not a major group, and it is a great resource, but I want to identify things that are going to be of use to all / many palaeontologists. Things a great many of us use or unite a lot of fields and I don’t think it does that.

      I might have to set up an additional list for archosaurs for things like this and the ones Henrique suggested.

  10. 13 220mya 09/02/2012 at 10:28 pm

    Morphobank does everything that Cladestore does, and way more. Its also had alot more inertia. Plus you can upload things like high resolution versions of your figures, supplementary figures, etc., which are all permanently archived. Alot of people aren’t aware of the use of Morphobank for non-phylogenetic visual data, but it has that capability. A number of forthcoming paleohistology papers that are coming out will make use of this.

    • 14 David Hone 10/02/2012 at 9:11 am

      All true now I’ve had a chance to explore Morphobanks. But looking aroundit for stuff I’m interested in at least, Cladestore did have a bunch of phylogenies it didn’t have, so it’s still a useful resource to know about.

      • 15 Jo Wolfe 10/02/2012 at 6:48 pm

        Yeah, the big advantage of MorphoBank vs. Cladestore is that it permits the linking of images to the matrix, i.e. you can have images to define your homology statements, or support each coding. You can actually construct your matrix from scratch in the cloud editor, and IMO it’s by far the most user-friendly way to do this (vs. MacClade, Mesquite, etc).

        We’re always looking to upload legacy matrices as well; the trick is a) receiving author permission (unfortunately) and b) getting them formatted properly. Unfortunately ‘stripped’ matrices won’t work – we require at least the names of characters and their states in the nexus/TNT file. It’s a lot of work, but hopefully rewarding if someone can actually build on a previously published matrix without having to type the thing or look up what the characters mean in random supplementary files.

  11. 16 Nick Gardner 09/02/2012 at 10:44 pm

    To my knowledge, Cladestore was never really well publicized, which probably is the reason behind its lack of notability.

  12. 17 Nick Gardner 09/02/2012 at 10:47 pm

    Thanks though for posting this link, Dave! There are some matrices here that would save one from having to redo from scratch!

  13. 18 Lars Dietz 10/02/2012 at 11:36 am
    Scans of old books and journals about biology/natural history. As of today they have 53633 titles.

  14. 19 Phoebe Cohen 10/02/2012 at 2:41 pm

    Check out – an amazing resource for North America, NZ, and deep sea stratigraphic records linked to the paleobiology database. Still in beta phase, but already really helpful and fun!

  15. 20 Tomasz Skawiński 10/02/2012 at 7:32 pm – phylogenetic definitions of many archosaur clade names (no updates since 2005 though…).

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