Thursday, March 06, 2014
IDCC14 notes, day 2: keynote Atul Butte
Sunday, March 02, 2014
IDCC14 notes, day 1: 4c project workshop
In stark contrast with the 'European' 2013 edition, held last year in my hometown Amsterdam, at this IDCC over 80% of the attendees were from the US. That’s what you get with a west coast location, and unfortunately it was not made up by more delegates from Asia and down under. However as the conference progressed it became clear that despite the vast differences in organisation and culture, we’re all running into the same problems.
IDCC 2014 Day 1: pre-conference workshop on 4C project
4cproject.eu is an EU financed project to make a inventory of the costs of curation (archiving, stewardship, digital permanence etc.) With a 2 year project span it’s relatively short. The main results will be a series reports, a framework for analysis (based on risk management) and the ‘curation cost exchange’, a website where (anonimized) budgets can be compared.The project held a one-day pre-conference workshop “4C - are we on the right track?” at which a roadmap and some intermediate results were presented, mixed with more interactive sessions for feedback from the participants. It didn’t always work (the schedule was tight) but still it was a day full of interesting discussions.
Neil Grindley noted that since the start of the project the goal has shifted from “just helping people calculate the cost” to a wider context. Beyond the actual cost (model) of curation: also the context, risks management, benefits and ROI. ROI is especially important for influencing decision makers, given the limited resources.
d3-1 - evaluation of cost models and needs gaps analysis draft
Cost models
Cost models are difficult to compare and hard to do. Top topics of interest: risks/trustworthiness, sustainability and data protection issues. Some organizations are unable or unwilling to share budgets. Special praise was given to the Dutch Royal Library (KB) for being a very open organisation for disclosing their business costs.The exponential drop of storage costs has stopped. The rate has fallen from 30-40% to at most 12%. It is impossible to calculate costs for indefinite storage. This lead to a remark from the audience: "we're just as guilty as the researchers really, our horizon is the finish of the project.” We have to use different time scales - you have to have some short time benefits, but also keep the long term in scope.
However, costs are much more than storage. Rule of a thumb: 1/2 ingest, 1/3 storage, 1/6 access. Preservation and access are not necessarily linked. Example is the LOC twitter archive which they keep on tape. Once (if) legal issues currently prohibiting opening this archive are resolved, access might be possible via amazon’s 'open data sets' where you pay for acces by using EC2. The economics work because amazon keeps it on non-presistent media and provides access, and LOC keeps it on persistent media but no access.
Other misc notes
The workshop included a primer on professional risk management, based on ISO 31000 standard. “Just read this standard, it's not very boring!”. Originally from engineering, risk management is now considered mature for other fields as well.
German Nestor project, really clear definitions on what a repository is, a useful resource comparable to the JISC reports:
www.crl.edu/focus/article/394
www.langzeitarchivierung.de/Subsites/nestor/DE/Home/home_node.html
Open Planets Foundation - great tools.
CDL DataShare is online - a really nice, clean interface.
Wednesday, February 22, 2012
The EJME plugin: improving OJS for articles with data
Who is EJME for?
Any journal that uses OJS for publishing and that wants to make it possible to have data files attached to articles (and as of December 2011, that's 11,500 Journals!).
What does it do?
Three things:
- improves the standard OJS handling of article 'attachments': files are available to editors and peers during the review process, and the submission process has been made (a little) easier;
- plays nicely with external data repositories: an attachment can be a link to a file residing elsewhere (but work just like an internal OJS attachment in the review and publishing stage), and an internal attachment that an author has submitted with the article can also be submitted to a data repository, creating a 'one-stop-shop' experience for the author;
- on publication, it automagically creates machine-readable descriptions of an article and its data files (in tech-speak: these are small XML files, so-called Resource Maps, in the OAI-ORE standard). These can be harvested by aggregators such as the Dutch site Narcis that can then do more great and wonderful things with it, for example slick visualizations.
Great, but I only want some of that!
That's perfectly possible. If you want only improved handling, they're included in the latest OJS version. The other two are in separate plug ins, install only what you need. Though I do recommend to install the resource map plug-in, it won't require any work after installing.
What does it cost?
Just like OJS itself, the plug-in is open source and free of cost. Installation is as easy as most OJS plug-ins.
What does the journal have to do?
Of course, software is only a tool. The real question is deciding what to do with it. Does the journal want a mandatory Data Access policy? Is there a data repository in the field to cooperate with? Once these questions are answered, the journal policy and editorial guidelines will need to changed to reflect them.
Why would my journal want data along with articles?
As science becomes more and more data-oriented (and that includes the humanities), publishing data along with articles becomes essential for the peer review system to function. There have been too many examples lately of data manipulation that would have been found out by reviewers if they would have checked the data. And for that, they need access to the data. Reviewers of course won't change their habits suddenly once data is available to them, but it's a necessary first step.
(There are many other reasons, both carrots and sticks, for the greater good or the benefit of journal and author, but IMHO this is the pivotal point).
Q: Why name it EJME, such a silly name?
Enhanced Journals Made Easy was a little optimistic, I admit. Enhanced Journals Made (A Little) Easier would have been better. You live and learn!
Want to know more about EJME? Get started with the documentation.
Saturday, July 02, 2011
OR11: Misc notes

I like going to conferences alone, it’s much easier to meet new people from all over the world than when you’re with a group, groups tend to cling together. With a multitracking conference like OR11 however, the downside is that there’s so much to miss. Especially since I like to check out sessions from fields I’m not familiar with. At OR11, I wanted to take the pulse of DSpace and Eprints, and not just faithfully stick with the Fedora talks.
In this entry, I focus on bits and bobs I found noteworthy, rather than give a complete description. I skip over sessions that were excellent but have already widely covered elsewhere (for instance at library jester) such as Clifford Lynch closing plenary.
“Sheer Curation” of Experiments: data, process and provenance, Mark Hedges
slides [pdf]
"Sheer curation" is meant to be lightweight, with curation quietly integrated in the normal workflow. The scientific process is complex with many intermediate steps that are discarded. The deposit at the end approach misses these. Goal of this JISC project is to capture provenance experimental structure. It follows up on Scarp (2007-2009).
I really liked the pragmatic approach (I've written this sentence often - I really like pragmatism!). As the researchers tend to work on a single machine and heavily use the file system hierarchy, they wrote a program that runs as a background process on the scientists’ computer. Quite a lot of metadata can be captured from log files, headers, filenames. Notably, it also helps that much work on metadata and vocabulary has already been done in the field in the form of limited practices and standards.
Being pragmatic also means discarding nice-to-haves such as persistent identifiers. That would require the researchers to standardise beyond their own computer and that’s asking too much.
The final lesson learned sounded familiar: it took more, much more time than anticipated to find out what it is the researchers really want.
SWORD v2
SWORD2: looks promising and useful, and actually rather simple. Keeping the S was a design constraint. Hey, otherwise we’d end up with Word, and one is more than enough!
Version 2 will do full Create/Read/Update/Delete (CRUD). Though a service can always be configured to deny a certain actions. It’s modelled on Google’s Gdata and makes an elegant use of Resource Maps and dedicated action URLs.
CottageLabs, one of the design partners, made a really introduction video to Sword v2 demonstrating how it works:
It looks really useful and indeed still easy (as per Einstein's famous quip, as simple as possible but not simpler). If you’re a techie, dive into SwordApp.org. If you’re not, just add Sword compliance to your project requirements!
Ethicshare & Humbox, two sessions on community building
Two examples of successful subject-oriented communities that feature a repository, each with some good ideas to nick.
Ethicshare is a community repository that aggregates social features for bioethics:
- one of the project partners is a computer scientist who studies social communities. Because of this mutual interest (for the programmer it’s more than just a job) they have had the resources to fine tune the site.
- the field has a strong professional society that they closely work with.
- glitches at beginning were a strong deterrent to success - so yes, release early and often, but not with crippling bugs!
- the most popular feature is a folder for gathering links, and many people choose to make them public (it’s private by default).
- before offering it to the whole site, new features are tried out on a small, active group of around 30 testers.
- for the next grant phase they needed more users quickly, so they bought ads. $300 for Facebook ads yielded for 500 clickthroughs, $2000 Google ads 5000. This (likely) contributed to number of unique visitors rising from 4k to 20k per month. Tentative conclusion: these ads cost relatively little and are effective for such a specialized subject, the targeting is really quite good.
Lessons from the UK based Humbox project:
- approach: analyse what scientists were doing already in real life, in paper and file cabinets, mimic it and extend it.
- "the repository is not about research papers, it is about the people who write them": the profile page is the heart, putting the user at the centre. Like Facebook’s, it has two distinct views: an outside version about you (to show off), and internal version for you (with your interests). This reminds me of the success of the original, pre-yahoo delicious, which also cleverly put self-interest first with the social sharing as a side-effect.
- Find a need that's not covered by existing systems: Humbox fills a need to share stuff, not just with students - for that the LCMS is the natural place to go to - but with colleagues, since the course-centric nature of LCMS’s tends to lock colleagues out.
- Most feedback came from community workshops. Participants often became local evangelists.
- Comments often were corrections. 60% of the authors changed a resource after a comment - and the 40% comments not leading to a correction also include positives, so the attitude towards criticism was quite positive.
- over 50% of users modified or augmented material from others, sometimes reuploading it to the site.
- Humbox only takes Creative Commons licenses, with an educational side-effect: some users indicated they also started looking in other places (such as flickr) for cc material as a result.
The Learning Registry: “Social Networking for Metadata”
slides [google docs]
I just want to mention this for the sheer scope and size of this initiative. It’s [explicative] ambitious.
The aim to gather all social networking metadata! To limit the scope, they won’t do normalising, or offer search or a query api, that's all left to the users of the gathered dataset. But all, they mean everything on the net: data, metadata and paradata (by which I understand they mean the relationships with other data).
Agreements are in the works with major partners (see last slide). The big elephant in the room was Facebook (no surprise, sigh) which wasn’t mentioned at all. (as I'm writing this, Google+ has just been announced, there is some hope after all of the slightly creepy evil eventually triumphing over the even more evil).
They call their approach a do-ocracy. Very agile design principles. Real-time everything in the open: all code and specs are written directly in Google Docs (table of contents, a google spreadsheet). NoSQL master-master storage system, well thought-out architecture, production will run on ec2. Everything will be open, except data harvested from commercial partners.
Something to keep an eye on: www.learningregistry.org.
Finally...
MODS is the new DC. In recent projects, MODS seems to have replaced Dublin Core as the baseline standard for metadata exchange. Interesting development.
Wednesday, June 29, 2011
OR11: New in EPrints 3.3: large scale research data, and the Bazaar.
Support for research data repositories
The new large scale research data is also a hallmark for pragmatic simplicity. EPrints avoid getting very explicit about subject data classification and control, taking a generic approach that can be extended.
Research data can come in two container datatypes, ‘Dataset’ and ‘Experiment’. A Dataset is a standalone, one-off collection of data. The metadata reflects the collection. The object can contains one or more documents, and must also have a read-me file attached, which is a human-oriented manifest, as, though machine-oriented complex metadata is possible, it would deter actual use.
The other datatype is Experiment. This describes a structural process that may result in many datasets. The metadata reflects process and supports the Open Provenance Model.
Where the standard metadata don’t suffice, one of the data streams belonging to the object can be an xml file. If I understood correctly, xpath expressions can then be used for querying and browsing. Effectively this unleashes the shackles of the standard metadata definitions and creates flexibility similar to Fedora. It's very similar to what we're trying to do in the FLUOR project with a SAKAI plugin that acts as a GUI for a data repository in Fedora. Combining user-friendliness with configurable, flexible metadata schemes is a tough one to pull off, I'll certainly keep an eye out on the way EPrints accomplishes this.
The Bazaar
The EPrints Bazaar is plug-in management system and/or an ‘App Store’ for EPrints, inspired by Wordpress. For an administrator it's fully GUI driven, versatile and pretty fool-proof. For developers it looks pretty easy to develop for (I had no trouble following the example with my rusty coding skills).
The primary design goal was that the repository including API must always stay up. They’re clever bastards: they based the plug-in structure on the Debian package mechanism, including the tests for dependencies and conflicts, which makes it very stable. Internally, they’ve run it for six months without a single interruption. Now that’s eating your own dog food!
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| Off the beaten track |
EPrints as a CRIS
The third major new functionality of 3.3 is CERIF import & export. Primarily this is meant to link eprints repositories automatically to CRIS systems, but for smaller institutions that need to comply with reports in CERIF format but don’t have a system yet, using eprints itself may suffice as pretty much all the necessary metadata is in there. The big question is whether the import/export would allow a full lossless roundtrip, as I joined this session halfway (after an enthousiastic tweet prompted me to change rooms) I might've missed that.
This sounds very appealing to me. Unfortuntaly, the situation in the Netherlands is very different, as a CRIS has been mandatory for decades for the Dutch Universities. Right now we’re in the middle of an European tender for a new, nationwide system, and the only thing I can say is that it’s not without problems. How I’d love to experiment with this instead in my institution, but alas, that won't be possible politically
As Les Carr couldn’t make it stateside, he presented it from the UK. The way this was set up was typical for the can-do attitude of the eprints developers: Skypeing in to a laptop which was put before a mike, and whenever the next slide was needed Les would cheerily call out ‘next slide please!’, after which the stateside companion theatrically reached out for the spacebar of the other laptop, connected to the beamer. Avoid neat technology for technology’s sake and keep it simple and effective.
Monday, June 20, 2011
DMP online is a great starting point (and one of the inspirations for CARDS) and this looks like the right group of partners to extend it into a truly generic resource. What's notable about the presentation is also the sensible reasons outlined for collaboration between this quite large group of prestigious institutions.All in all, something to keep an eye on.
Wednesday, May 27, 2009
OR09: Keynote by John Wilbanks
Locks and Gears: Digital Repositories and the Digital Commons - John Wilbanks, Vice President of Science, Creative Commons
Great presentation - in content as well in format. Worth looking at the slides [slideshare - of a similar presentation two weeks earlier]. [Which was good, because it was awkwardly scheduled at the end of the afternoon, that's great with a fresh jetlag, straight after the previous panel session without as much as a toilet break.]
The unfortunately familiar story of journals on the internet, scholars' rights eroding, which causes interlocking problems that prevent the network effect.
Choice quotes:
“20 years ago, we would have rather believed there be a worldwide web of free research knowledge, than Wikipedia.”
"The great irony is that the web was designed for scientific data, and now it works really well for porn and shoes."
The CC licenses are a way of making it happen with journals. However, for data even CC-BY is making it hard to do useful integration of different datasets. Survey of 1000 bio databases: >250 different licenses! Opposite law of open source software: the most conservative license wins.
Example of what can happen if data is set free: Proteomecommons.org: bittorent for genomes. Thanks to CC Zero.
What can we do?
Solve locally, share globally.
Use standards. And don’t fork them.
Lead by example.
Q: opinion on wolfram alfa? Or Google Squared?
A: pretty cool, doubts about scaling. It may be this or something else, rather open source than ‘magic technology’. But it’s a sign that the web is about to crack.
“The only thing that’s proven to scale is distributed networks.”
(my comment - with an estimated 500.000 servers, that is precisely what Google is...)
Tuesday, May 26, 2009
OR09: NSF Datanet-curating scientific data
The first non-split plenary (why a large part of the first two days consisted of 'split plenaries' baffled me, and I was not the only one).
Two speakers, two approaches. First John Kunze from UCDL, focussing in the microlevel with a strategy of keeping it simple. "Imagining the non-repository", "avoid the deadly embrace" of tight standards: decouple by design, lower the barrier of entry.
One of the ways to accomplish this is by staying lo-tech: instead of fullblown database systems, use a plain file system and naming conventions: pairtree. I really like this approach. I've worked in large digitization projects with third parties delivering content on harddisks. They bulk at databases and complicated metadata schemes, but this might just be doable for them. Good stuff.
CDL has a whole set of curation microsystems, as they call it. I'm going to keep an eye out for this.
The second talk, by Sayeed Choudhury (Johns Hopkins), focussed on the macro level of data conservancy. This was more abstract, and he started out with the admission that "we don’t have the answers, there are unsolved unknowns - otherwise we wouldn’t have gotten that NSF grant".
Interesting: one of the partner institutions (not funded by NSF) is Zoom Intelligence – a venture capital firm, interested in creating software services on research data. First VS's bought into ILS, now they pop up here... we must be doing something right!
Otherwise, the talk was mostly abstract and longer term strategy.
Sunday, May 24, 2009
OR09: PEI's Drupal strategy for VRE and repositories
Small province in Canada, middle of nowhere, pop 140k, only uni on the island. UPEI is doing very some good stuff, made some radical choices. They fundamentally transformed the library from traditional staff to techies. Number of staff didn’t change (25), but the number of techs increased from 1 to 5, plus a pool of freelancers.
VRE's using Drupal
Strong push for VRE’s, using Drupal as platform. Low entry barrier: any researcher can request one! All customisations are non-specific as a rule, so all users benefit in the end. If researcher brings additional funding, contract devs are hired to speed up the process.
Some clients have developed rich Drupal plugins themselves (depends on a willing postgrad :-)
Currently 50+ VRE’s. Example of a globe-spanning VRE: Advancing Interdisciplinary Research in Singing
But the same environment is also used for local history projects with social elements (“tag this image”).
Why going opensource? Improves code and documentation quality by emberrassment factor: “Going opensource is like running through the hotel at night naked – you want to be at least presentable”.
Repository: Drupal+Fedora=Islandora
PEI developed Islandora as frontend for Fedora repository. However, from the users POV it is completely hidden: they log in to the VRE, this silently handles depositing in the rep.
Both Drupal and Fedora are ‘strong systems’ with a lot of capabilities. However by definition all data and metadata go in Fedora, to separate data from application layer and make migration possible. This needs to be strongly enforced as some things are easier in Drupal.
Very neat integration betwee data objects in repository and VRE: Researchers can search specifically within the objects, as in “search for data sets in which field X has value between 7 and 8”. Done by mapping the data to an xml format, then mapping xml fields to search params. For fields where xml data formats are available and commonly used this is a real boon (example of marine biology).
BTW fifteen minutes in the talk I connected the acronym PEI with the name Prince Edward Island. PEI must be so famous in the repository world that it either needn't be explained at all, or that it was mentioned so briefly that it slipped me by...
OR09: Purdue's investigation on Research Data Repositories
OR09 day 1, session 2a: Michael Witt (Purdue University) "Eliciting Faculty Requirements for Research Data Repositories
Preliminary results of investigation in what researchers want regarding data (repositories). Some good stuff. Hope the slides will be published soon - or the report for that matter.
See Seans weblog for the ten primary questions, good for self-evalution also. Mark Leggott then quickly added an additional 11th question to his slideshow - how much is in your wallet...
Method: interviews and followup survey with twenty scientists, transcribed (using Nvivo). “It was like drinking from a firehose.” For each, a “data curation profile” was created, with example data & description. Will beinteresting when it comes out.
OR09: on subject based repositories
Open Repositories 2009, day one, session 1b.
Phew! OR09 is over, and my jetlag almost. An intense conference that was certainly worth it, the content was generally interesting and well-presented. I'll be posting my conference notes here the coming few days.
First session on Monday morning were two talks on two subject based repositories. The planned third one, on a Japanese one, was cancelled - unfortunately as I know very little of what’s happening there regarding OA.
First came Julie Ann Kelly (University of Minnesota) on AgEcon, a repository for Agricultural Economics, a field with a strong working paper tradition. It was set up in the gopher days (not so surprising, as the critter originated in Minnesota).
Interesting was the reason: in this fields, working papers are citable, but the reference format was a mess.
Even more interesting: because of this, it also became the de facto place for depositing appendices to articles - datasets! The repository accepts them and they have the same citing format. There is a lesson here... solve a real problem, and content will come.
Usage statistics: only 53% of downloads comes from people, 43.6% is googlebot (rest other spiders). 66% of visitors come through google straight to results, not through the frontend anymore. Then 19% are some other search engines: leaves 14% coming through front.
Further notes:
Why is life easier in a subject repository?
- Focussed topic makes metadata easier, common vocabularies exists etc.
- Recruitment (of other institutions) is easier (specialists in one profession tend to meet frequently, recruiting can piggyback on conferences etc).
And why is it harder?
- organising the community is hard work - 170 institutions with each between 1 and 300 submitters creates a lot of traffic on quality issues. They frequently hire studens for the correcting.
Minnesota is consolidating its repositories from 5-6 different systems to Islandora. AgEcon will be one of them.
They want to use this Drupal based system also to add social networking, akin to Ethicshare. Ethicshare is interesting: a social citation manager (a la Citeulike/Bibsonomy) plus repository plus social network plus calendar and then some more, for a specific field of study, in this case ethic research. Commoditisation coming?
The second subject repository was on Economists Online, presented by Vanessa Proudman of Tilburg University. Interesting to see this is in many ways the opposite approach. EO is a big European project that works top-down, tries to get the big players aboard first as incentive for the others, and emphasizes quality above all. Whereas AE was a grassroots bottom-up model, that empowered small institutions.
It's a work in progress, only mockups shown. These look slick, with a well thought-out UI. Interesting: with every object in the result list, statistics will be shown inline (ajax), and can be downloaded in multiple formats.
Small pilot with 10 datasets per participating institution, DDI format, Dataverse as preferred solution. Provenance of datasets is very complicated: there are many contributors to the data life cycle, dataset owners, sources, providers, all must be accredited.
Like AE, EO stresses that subject-based repositories have different characteristics. They will organize a dedicated conference on subject repositories in january 2010 in London, as they note that the subject rarely comes up at general repository conferences.
Interest in attending: mail subjectrep_parts@lists.uvt.nl


