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Egon Willighagen › Likes

Dan Gezelter
Cameron Neylon
I am rapidly coming to the conclusion that repositories are largely designed to make it as difficult as possible to find out whats in them, and what it actually is...I have 36,000 DOIs and I'd like to know whether they are in a repository...
Yeah, good luck w that, as far as I know. Though I'd love to be wrong! - Heather Piwowar from iPhone
*shrug* yeah, basically. author-supplied metadata, need SQL knowledge and back-end server access to batch-fix anything, no version-spanning identifiers, no agreed-upon version-linking metadata... the scaffolding to make this shit work just isn't there. - RepoRat
NISO is working on the version-linking problem, but, you know, *NISO*... - RepoRat
...and OAI-PMH...[shudder]...well not the standard so much as the way its implemented in apparently 25 subtly different ways, and that's before people start shifting the endpoint without notifying anyone - Cameron Neylon
Version linking problem will likely get solved by Crossref and either UK repo community or SHARE getting itself together. I don't have a problem with either route - lets get DOIs or handls for repository content and then we can set up some sort of global "relates-to/is-a-version-of" service somewhere. People are already gathering that data anyway - just its all over the place. - Cameron Neylon
Can you do title of article matching? I know that won't work in many cases. Maybe 80-95% of the time? - Joe - Systems Analyst
OAI-PMH is shite. It didn't have to be, but that's what happens when you dump something into the world and then abandon it, LAGOZE AND VAN DE SOMPEL. - RepoRat
Title matching is problematic and we essentially have to do it via a pull of the entire repo content as well as essentially no-one currently provides a search API. I can see why people keep building things like CORE and BASE as a way around these problems but...[sigh] - Cameron Neylon
Once I've got some info we can then do fun stuff (we could do more fun stuff if most publishers weren't just as crap at providing good metadata of course but one battle at a time) - Cameron Neylon
when you say nobody provides an API you mean repos? If so, are there any repo platforms that do,and if so are they doing what you need? - Kubke
So eprints and DSpace both surface an OAI-PMH service by default. But they tend to do so in very inconsistent ways. What no-one seems to do (or at least document) is a service by which I can hit a repo with an identifier like a DOI and say "do you have full text for this?" This seems to me rather fundamental to the point of the exercise...really not keen on the idea of downloading the entire catalogue for a few thousand repos... - Cameron Neylon
How's a repo supposed to know? In a self-archiving context, faculty won't put in DOIs for stuff they deposit (even assuming it has one yet, which a pre/postprint often won't). Title/author matching is dicey as hell. - RepoRat
Assuming mediated deposit, that lookup is pretty time-consuming if done manually. There is no service that automates it that I'm aware. - RepoRat
No you're right there isn't. To be honest my problem isn't so much that people don't use OAI-PMH dc:identifier to provide a DOI, but more that there is no way to lookup. I'll live with title/author matching as a starting point but what's really problematic is there's no way to say "here's a bunch of articles, tell me which ones you (think you) have, and tell me of those which you have full text for" - Cameron Neylon
That said, a good deposit path would involve triggering off bibliographic databases, that info would often include enough to determine a DOI. And of course the Crossref API itself is pretty good at matching a freetext citation (authors plus title plus journal). It could be done (and some repos do it) - Cameron Neylon
but whatever would anyone need a repository query API for?!?! The Great Information Scientists didn't build one, so obviously it's not needed! Everybody uses OAI-PMH, so that MUST mean it's the bee's knees!</sarcasm> - RepoRat
(Do not ask me about the NISO conference call where people were shocked, SHOCKED, that I do not think much of OAI-PMH. Just do not ask me about that. But the last sentence in my previous comment was pretty much verbatim from that call.) - RepoRat
Yes. Well. We're likely to be shortly publicising how the best repositories make it straightforward to determine policy compliance and how others...well...you can figure that out. Never would have thought I'd become a fan of league tables... - Cameron Neylon
Go for it. - RepoRat
Have you played with https://prospect.crossref.org/ at all? I could see this helping... but at this early date possibly not much. - RepoRat
Christina Pikas
APIs for news data? Does anyone know of any from L-N, ProQuest, NewsBank, PressDisplay or other sources?
Barry Hardy
First ToxBank Tutorial released - http://bit.ly/LvzUSK
Pierre Lindenbaum
Hi FriendFeed, Twitter is down.
Barry Hardy
Goodbye Patrik, we will miss you. - http://barryhardy.blogs.com/cheminf...
Patrik has a friendly guy indeed. A loss indeed :( - Egon Willighagen
Christina Pikas
Jan Velterop makes a good point on liblicense: transferring your copyright *is* paying the publisher. you're giving them something of value to get the publishing service in return. better to just pay article page charges so it's transparent and you can get cc-by.
in which case toll-access publishers are getting paid twice. f*** that. - RepoRat
Jan doesn't understand how publishing in the hard sciences works then, because most biomedical journals charge publications fees and demand copyright transfer, for an article that will be locked up. - DJF
^This. In my (limited) experience, copyright transfer is standard for biomedical journals, even open-access ones like Plos One. - Jessie
PLOS One doesn't need a copyright transfer. All of their stuff is CC-BY as far as I know. But, I am sure many other OA publishers are happy to have copyright. - Joe - Systems Analyst
Jan knows all about publishing - he's been in publishing for more than 20 years. He wasn't saying that's all you're paying them, he's saying you're paying them twice (or three times. - Christina Pikas
I agree with him, but practically that's not going to convince researchers who can't put their copyright on a balance sheet. It's not necessarily (though sometimes is) that they have moral objections to paying APC, it's that they *don't have the money* because the research budget's all used up. - Deborah Fitchett
Yes. I have been talking with people about this, and it is kind of amazing this realization is not wide-spread. - Egon Willighagen
Christina Pikas
as i skipped through an email (tl;dr) someone else just asked S.H. to elaborate on a listserv. o_O
nooooooooooooooooooooooo - RepoRat
Oh dear. - Kirsten
Though I have to admit I'm enjoying his takedown of Beall's latest craziness. Where's my Soros funding?!? - Sarah from FreshFeed
Erg. (Sarah: Missed that, probably because I avoid S.H. as much as possible.) - Walt Crawford
I would watch a Harnad/Beall mud-wrestling match. Yep. Would root against 'em both. - RepoRat
Beall has gone extra extra crazy this time. Maybe he'll actually lose all credibility now? - Sarah from FreshFeed
THAT WOULD BE NICE. How can we make it happen? - RepoRat
Extra crazy? - Joe - Systems Analyst
Much as I hate to say it where either Beall or SH is concerned: Link? - Walt Crawford
See the SK (as much as I hate to say it). On phone so can't quite get into the links to Harnad. - Sarah from FreshFeed
My favorite part is that he calls OA a conspiracy of well compensated Soros funded European autocrats. - Sarah from FreshFeed
This thread is all in code to defeat NSA surveillance, right? #NotaClue - Jkram|ɯɐɹʞſ from Android
Ah. First time I've looked at SK in months (and it was in a sidebar). Bookmarked the "article" but only read the first couple of paragraphs, which were enough. How many bends must a man go around before he's mostlin ignored? (Apologies Bob Dylan.) - Walt Crawford
*sigh* if we seeded that into the academe-blog-sphere -- Mike Taylor or the Eisens or somebody -- with a seasoning of anti-librarian sentiment, I bet it'd go viral. I am SO NOT VOLUNTEERING to do that, however. - RepoRat
oh, I know, feed it to Peter Murray-Rust; he loathes librarians. - RepoRat
Thanks, Joe. The paper is hilarious! - Egon Willighagen
Now, Beall will need at least ten rational, understandable, well-reasoned and coherent articles to convince anybody that he is not mentally ill. - Björn Brembs
I am wondering at the quality of the peer review process at that journal...maybe its.... - Cameron Neylon
Ah turns out that section is not peer reviewed. But you wouldn't know that if you just arrived at the paper. - Cameron Neylon
Kubke
After an 1893 book which seems to be at the Library at Unversidad de Barcelona - Am afraid neither ILL nor #Icanhazpdf will be able to help - also not in the catalogues of my antiquarians. Grrrr......
Put it up in here. You never know. Maybe biodiversity heritage library - Christina Pikas from iPhone
What book is it? - Joe - Systems Analyst
Thanks - Biodiversity Catalog doesnt have it (didn know of about that) - Neither does Hathi Trust (which has a lot of v. good old neuroscience books I have been wanting to get my hands on!) - The main one is CL Sala Pons, La corteza cerebral de las aves, Madrid 1989 (only found at University of Barcelona). Also interetsted in Pedro Ramon y Cajal's Trabajos de la seccion de tecnica anatomica de la facultad de medicina de Zaragoza, 1889. - Kubke
Do you need the full book, or just a part? That is, can we recruit someone in Barca to copy the pages you want? - Egon Willighagen
well, worldcat knows of 2 other copies but probably no better. One is in Bibliothèque interuniversitaire de santé and the other is at Royal College of Surgeons of Engineer (which is not listed as a lender) - Christina Pikas
huh. appears to be his thesis? and bound with other pamphlets by the same author? maybe that would be the way to look? - Christina Pikas
I don't think so - at least not in the way we think of theses today as a document related to a degree. I'd suspect the word "thesis" (at least in spanish) was used to describe a type of book that was not quite a monograph, and it might have stuck. - Kubke
@Egon - we just need a part - but of course we don't know what page the info we are looking for is. We are emailing our colleagues in Spain so we can send them a picture of what we are looking for and hopefully they'll find a similar illustration in the book :) - Kubke
Texture of the Nervous System of Man and the Vertebrates was just reprinted in English: http://link.springer.com/book... but that's more recent. - Christina Pikas
@Christina - ah yes, forgot about the french one, somehow worldcat didnt return the the RC of surgeon that I remember. We are after a colleague in Valencia who might be able to help us get to the Barcelona copy or may know of someone who has a copy on their shelves (my shelves have several of these types of books dating to 1700's!) We actually got the citation from a 1904 book that I have a facsimile of. Oh well, no one can accuse me of not trying to do proper attribution :) - Kubke
What a beauty! A colleague of ours from University of Valencia got us and sent us the pdf! Nothing like reading an 1893 neuroanatomy paper to underscore how little we have progressed! We basically know as much today about these odd neurons we are looking at as Sala Pons and the Cajal brothers did at the end of the 19th century! - Kubke
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Rich Apodaca
Re: Shorten Long IUPAC Chemical Names with this One Weird CSS Trick - http://metamolecular.com/blog...
Noel O'Boyle
Antony Williams
Chemical Validation and Standardisation Platform (CVSP) goes live! - http://www.chemspider.com/blog...
Christina Pikas
PubMed Commons? First I'd heard? http://www.ncbi.nlm.nih.gov/pubmedc... "a system that enables researchers to share their opinions about scientific publications. Researchers can comment on any publication indexed by PubMed, and read the comments of others"
First I've heard of it. Interesting. - RepoRat
Hmmm, I saw some other "more full text than pub med" thing last week but not sure I've seen this. - Hedgehog from Android
I think it sucks that just the NIH/Wellcome elite is allowed in - seems a bit discriminatory. Big boys club - again. - Kubke
I thought it was anyone who had an article indexed by pubmed? So I'm not eligible but I'm guessing everyone else on this thread is - Christina Pikas from iPhone
So glad they have *another* PMC acronym now...also waiting to see how long it takes Scholarly Kitchen to have a kitten about it. - Rachel Walden
@ Christina - my understanding is yes, indexed author, but if not under the NIH/Wellcome then you cannot register - someone has to invite you - too second class citizens for my taste. - Kubke
Christina Pikas
the seductive thing about coding is solving the problems... the point when you've figured it out, and it seems easy, when you were beating your head against the wall trying to get there.
conversely... the part when you can't figure out what's wrong is slightly soul sucking - Christina Pikas
I'm finding paracetamol to be of great help right now :) - Kubke
Barry Hardy
US Government shutdown is blocking international collaboration - http://barryhardy.blogs.com/theferr...
Barry Hardy
OpenTox Euro 2013 Awards - http://bit.ly/19424vK
Carmen Drahl
Use Twitter #chemnobel for questions - Countdown to #Chemnobel - http://www.youtube.com/watch...
Use Twitter #chemnobel for questions - Countdown to #Chemnobel
Play
Christina Pikas
some asshole at mpow (yeah, i guess there must be one here) got us cut off from Wiley by using a bot to batch download... we're gonna hunt 'im down. grrrr.
We get cut off from something at least once or twice a year. - John Dupuis
but you can't just use our wireless - there's no guess access without a password so this was a staff member. - Christina Pikas
We get cut off maybe once every 3 to 4 myths to some major resource due to that. - aaron from YouFeed
This has happened to us because a student shared their login information with somebody from their home country. - kaijsa
This has happened to us because of "Find Fulltext" in EndNote. - Meg VMeg
Huh, I wonder if we might run into that EndNote problem here. I helped a lab do that with 200+ articles but that was 6 months ago and we haven't had any shutoff. With some of the Endnote files I've seen though with several thousand articles... - Hedgehog
Someone claimed it was Endnote that caused them accidentally to systematically download every article from every issue of a certain journal. We weren't able to replicate how this could happen and the logs looked a lot more human-speed than computer-speed. But they seemed to have learned the lesson that we can hunt them down, so. - Deborah Fitchett
Why not hunt Wiley down? Seriously, some issues are just damn interesting and must you read them online and not on the train?? Seriously, hunting down research who want to read literature, as a librarian?? What about informing him that Wiley does not appreciate them reading the journal? - Egon Willighagen
this was 40,000 articles, apparently. I'm not sure how Wiley's alarms didn't trip earlier than that. - Christina Pikas
oh hey... not an asshole at all :) our infosec people traced it down and they just hit the button once and wiley's server went bonkers... now to get turned back on! - Christina Pikas
So just to confirm. This was Wiley's fault on the server side? - Cameron Neylon
as far as my infosec guys can tell, yes - Christina Pikas
ADDED VALUE. - RepoRat
and we are still cut off. and now people starting to pick up their pitchforks and torches... - Christina Pikas
we're back on again. - Christina Pikas
*high five* - Meg VMeg
Barry Hardy
Open Data, Open Source, and Open Standards for Toxicology, chaired by Egon Willighagen (Maastricht University) - http://barryhardy.blogs.com/theferr...
Barry Hardy
OpenTox Euro 2013 workshops running - http://barryhardy.blogs.com/theferr...
Pierre Lindenbaum
Pierre Lindenbaum
Presentation : File formats for Next Generation Sequencing - http://plindenbaum.blogspot.com/2013...
Christina Pikas
Best/recommended ontology for bibliographic data? I see bibframe and bibo - looking for an owl file ... Mostly to describe journal articles (not whole books) - Tia
oof. I think there isn't one besides BIBO. I see calls for one pretty often! - RepoRat
bibo it is! thanks (we could always make our own, but eek) - Christina Pikas
Yeah, BIBO is the way to go. Also check CiTO, aka the Citation Typing Ontology... - Egon Willighagen
I looked at cito but I think it covers different things. Egon- I might need some help with som chem ontologies,too, but I'll go out to chminf. Thanks! - Christina Pikas from iPhone
crowdsourced folksonomy *ducks* *runs* - awd
Christina, yeah, CiTO is really about citing things, and how and why that citation exists. But I like to think of a library is something we use and refer to :) About CHEMINF, yeah, please do! Let me know if I can assist with that ontology, or any other life science ontology. - Egon Willighagen
I'd look at the British Library's data model for serials. http://www.bl.uk/bibliog... They don't use a single ontology to describe journals, and you might choose not to adopt every aspect of their model, but I think it's a very good one. - Laura Krier
Antony Williams
Southampton University internships to transfer thesis data into LabTrove and ChemSpider - http://www.chemspider.com/blog...
Noel O'Boyle
Unavailable by request - Do you have to ask? - http://baoilleach.blogspot.com/2013...
Barry Hardy
OpenTox USA 2013 program and goals - http://barryhardy.blogs.com/theferr...
Joe - Systems Analyst
Should we ditch the journal impact factor on Thursday? http://news.sciencemag.org/scienti...
Why wait? - Deborah Fitchett
The online session "Live Chat: Should We Ditch Journal Impact Factor?" is on Thursday. I conflated the two to make it stand out. But, if you want to wait until Friday to ditch the impact factor, that is fine with me. - Joe - Systems Analyst
Christina Pikas
and honestly, i'll start working soon :) but i just got an email from maryland to "impact a student this fall"... so they want me to knock one over to make them fall? only if they piss me off!
Kubke
ok we all played in G+ time to come back to FF....
You weren't included dear Graham cause you never left!!!!! :) Just miss the conversations and feeling a bit lost...... - Kubke
I'm amazed it is still running... if only they would open development... - Egon Willighagen
Daniel Mietchen
Feature request: Search by license - http://www.science3point0.com/evomri...
About the benefits of a search-by-license feature at PubMed: Open Access comes in many flavours, as highlighted by Cameron Neylon some hours ago. One of these flavours is the type of license under which the content is made available — one of the intersections of science and law. To facilitate navigation in these waters, it would be good if 1. all articles were clearly tagged (for both humans and machines) with their respective license (the same argument for data is central to the Panton Principles, by the way) 2. the license type could be used as a parameter in searches across articles or their metadata, or aggregations thereof (as is possible on Flickr and BioTorrents, and requested at Vimeo). - Daniel Mietchen
Thank you! Plenty to ponder in your response, thanks for posting it. - Rachel Walden
Reply from PubMed just came in: "The data to which I believe you are referring is not contained on PubMed/MEDLINE records. It cannot, therefore, be made searchable." It seems I should have submitted to the PMC helpdesk at http://www.ncbi.nlm.nih.gov/sites... . Just did so. - Daniel Mietchen
Took a while, and a lot of nudging from Daniel, but PMC search by license is now a reality: http://www.ncbi.nlm.nih.gov/pmc.... - Chris M
yay! - Kubke
daniel, do you have a new url for that blog post? - Kubke
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