Posts Tagged ‘Technology/Internet’
Sunday, May 6th, 2018
The site fairsharing.org is a repository of information about FAIR (Findable, Accessible, Interoperable and Reusable) objects such as research data.
A project to inject chemical components, rather sparse at the moment at the above site, is being promoted by workshops under the auspices of e.g. IUPAC and CODATA and the GO-FAIR initiative. One aspect of this activity is to help identify examples of both good (FAIR) and indeed less good (unFAIR) research data as associated with contemporary scientific journal publications.
Here is one example I came across in 2017.[1]. The data associated with this article is certainly copious, 907 pages of it, not including data for 21 crystal structures! The latter is a good example of FAIR, being offered in a standard format (CIF) well-adapted for the type of data contained therein and for which there are numerous programs capable of visualising and inter-operating (i.e. re-using) it. The former is in PDF, not a format originally developed for data and one could argue is closer to the unFAIR end of the spectrum. More so when you consider this one 907-page paginated document contains diverse information including spectra on around 60 molecules. Thus the spectra are all purely visual; they are obviously data but in a form largely designed for human consumption and not re-use by software. The text-based content of this PDF does have numerous pattens, which lends itself to pattern recognition software such as OSCAR, but patterns are easily broken by errors or inexperience and so we cannot be certain what proportion of this can be recovered. The metadata associated with such a collection, if there is any at all, must be general and cannot be easily related to specific molecules in the collection. So I would argue that 907 pages of data as wrapped in PDF is not a good example of FAIR. But it is how almost all of the data currently being reported in chemistry journals is expressed. Indeed many a journal data editor (a relatively new introduction to the editorial teams) exerts a rigorous oversight over the data presented as part of article submissions to ensure it adheres to this monolithic PDF format.
You can also visit this article in Chemistry World (rsc.li/2HG7lTk) for an alternative view of what could be regarded as rather more FAIR data. The article has citations to the FAIR components, which is not published as part of the article or indeed by the journal itself but is held separately in a research data repository. You will find that at doi: 10.14469/hpc/3657 where examples of computational, crystallographic and spectroscopic data are available.
The workshop I allude to above will be held in July. Can I ask anyone reading this blog who has a favourite FAIR or indeed unFAIR example of data they have come across to share these here. We also need to identify areas simply crying out for FAIRer data to be made available as part of the publishing process beyond the types noted above. I hope to report back on both such feedback and the events at this workshop in due course.
References
- J.M. Lopchuk, K. Fjelbye, Y. Kawamata, L.R. Malins, C. Pan, R. Gianatassio, J. Wang, L. Prieto, J. Bradow, T.A. Brandt, M.R. Collins, J. Elleraas, J. Ewanicki, W. Farrell, O.O. Fadeyi, G.M. Gallego, J.J. Mousseau, R. Oliver, N.W. Sach, J.K. Smith, J.E. Spangler, H. Zhu, J. Zhu, and P.S. Baran, "Strain-Release Heteroatom Functionalization: Development, Scope, and Stereospecificity", Journal of the American Chemical Society, vol. 139, pp. 3209-3226, 2017. https://doi.org/10.1021/jacs.6b13229
Tags:above site, chemical components, Findability, Human behavior, Information, Information architecture, Information science, Institutional repository, journal data editor, Knowledge, Knowledge representation, Open access, Open access in Australia, Oscar, PDF, recognition software, Technology/Internet, Web design
Posted in Interesting chemistry | 2 Comments »
Wednesday, March 7th, 2018
C&EN has again run a vote for the 2017 Molecules of the year. Here I take a look not just at these molecules, but at how FAIR (Findable, Accessible, Interoperable and Reusable) the data associated with these molecules actually is.
I went about finding out as follows:
- The article DOI for all seven candidates was linked to the C&EN site.
- From there I manually tracked down the Supporting information
- Some of this SI gave a CCDC deposition number for crystal structure data for the molecule in question. The easiest way of going directly to the data was to use the search.datacite.org search engine and to enter the keywords CCDC + deposition number. This gives a DOI for the data, examples of which are included in the table below.
- In other examples, I used the CSD Conquest search program and entered the names of 2-3 of the authors of the articles. This also worked well.
- Most of the SI files, downloaded as PDF files also had static images of NMR spectra included. This is not active data, and hence does not fulfil the F and I of FAIR, and probably the A as well. None of it is FAIR as defined by my post here although it is actually really easy to make it so. One of the examples had ~116 spectra so unFAIRed.
- In another example there was also computational data, included simply as a set of XYZ coordinates and again contained in the PDF file. This too is not really FAIR, since one has to know how to extract it from this container and repurpose it. It also represents a tiny subset of the data potentially available.
The FAIRness of the data for these molecules of the year is largely rescued by the crystal structure data deposited with the CCDC in their CSD database and rendered F of FAIR by the persistent identifiers such as the (parochial) deposition numbers or the more general DOI. Now if the NMR and computational data were also covered in this way, we would be making great progress. There are of course many other types of data included with these examples, and procedures for making such data also FAIR have to be worked out by the community.
In order to construct the table above, I had to put about two hours of effort into tracking down the items (and this only because I have done this sort of search before). Perhaps next year I might persuade C&EN to include such a table in their own article!
Tags:Carotenoids, Chemistry, Epoxides, Macrocycles, Organic chemistry, Organofluorides, PDF, Peptides, search engine, search program, search.datacite.org search engine, Technology/Internet
Posted in Chemical IT, crystal_structure_mining, Interesting chemistry | No Comments »
Tuesday, January 23rd, 2018
Another occasional conference report (day 1). So why is one about “persistent identifiers” important, and particularly to the chemistry domain?
The PID most familiar to most chemists is the DOI (digital object identifier). In fact there are many; some 60 types have been collected by ORCID (themselves purveyors of researcher identifiers). They sometimes even have different names; in life sciences they tend to be known instead as accession numbers. One theme common to many (probably not all) is that they represent sources of metadata about the object being identified. Further information if which allows you (or a machine) to decide if acquiring the full object is worthwhile. So in no particular order, here are some of the things I learnt today.
- Mark Hahnel noted the recent launch of the Dimensions resource which links research data with other research activities; I have not yet had a chance to learn its capabilities, but it seems an interesting alternative to other stalwarts such as eg Google Scholar etc.
You can try this example: https://app.dimensions.ai/discover/publication?search_text=10.6084&search_type=kws&full_search=true which retrieves articles in which the data repository with prefix 10.6084 (Figshare) is cited. Try also the prefix 10.14469 which is the Imperial College repository.
- Andy Mabbett talked about the deployment and use of persistent identifiers (the Q numbers) in Wikidata, which increasingly underpin the basis for the various flavours of Wikipedia. He also noted their use of some 50 different identifiers.
- Johanna McEntyre noted some 5M published articles in life sciences which reference 1M+ ORCID identifiers, easily the domain with the fastest uptake of this type. Also noted was the new FREYA project; aiming to connect open identifiers for discovery, access and use of research resources.
- Tom Gillespie talked about RRID, or Research Resource Identifiers. Included in this are hardware, including instruments and with around 6000 RRIDs systematized so far. They argue this area promotes both the A and I of FAIR (accessible and inter-operable). Of course A and I mean many things to many people.
- Several other presentations talked about the finer detail of metadata, such as sub-classifications into e.g. descriptive/admin/technical, but I did rather miss demos showing how search queries of such fine-grained metadata could be constructed.
Apart from the presentations themselves, PIDapalooza is unusual for some other activities. Thus you could go get your PIDnails done, with a selection of 8 or so tasteful logos to choose from. There will be tattoos tomorrow (this is a conference for younger people after all). I may grab a photo or two to provide evidence!
Tags:Academic publishing, Andy Mabbett, Digital Object Identifier, Identifiers, Imperial College, Index, Information science, Johanna McEntyre, Knowledge, Mark Hahnel, ORCiD, Persistent identifier, Publishing, Quotation, researcher, Scholarly communication, SciCrunch, search engines, Technical communication, Technology/Internet, Tom Gillespie
Posted in Chemical IT | 1 Comment »
Thursday, December 7th, 2017
FAIR data is increasingly accepted as a description of what research data should aspire to; Findable, Accessible, Inter-operable and Re-usable, with Context added by rich metadata (and also that it should be Open). But there are two sides to data, one of which is the raw data emerging from say an instrument or software simulations and the other in which some kind of model is applied to produce semi- or even fully processed/interpreted data. Here I illustrate a new example of how both kinds of data can be made to co-exist.
I will start with a recent publication[1] with the title Crystallographic Snapshot of an Arrested Intermediate in the Biomimetic Activation of CO2. The nature of this intermediate caught the eye of another research group, who responded with their own critique[2]‡ along with the comment “However, since we have no access to the original crystallographic data …” They might have been referring to the semi-processed data (containing the so-called hkl structure factors) but they may also have been alluding to the raw image data captured directly from the diffractometer cameras. That traditionally has not been available via the CSD (Cambridge structural database), but would be required for a complete re-analysis of the crystal structure. Now the first example of how both FAIR (processed) data and raw data can co-exist has appeared.
The latest version of the CSD database shows an entry resulting from the following publication[3] and the deposited data has its own DOI there (10.5517/ccdc.csd.cc1n9ppb). That entry in turn has a DOI pointer to the Raw data (10.14469/hpc/2300) held in a different location and the pointer is reciprocated (⇌) with the latter pointing back to the former. Both datasets point to the original article, thus completing a holy triangle.†
There is more. The Raw dataset (10.14469/hpc/2300) declares it is a member of a superset, called Crystal structure data for Synthesis and Reactions of Benzannulated Spiroaminals; Tetrahydrospirobiquinolines (10.14469/hpc/2297) where you can find information about six other related structures. That collection is in turn a member of a superset called Synthesis and Reactions of Benzannulated Spiroaminals; Tetrahydrospirobiquinolines (10.14469/hpc/2099) where DOIs to other types of data associated with this project can be found, such as Computational data (10.14469/hpc/2098) and NMR data (10.14469/hpc/2294). Although a human can with some determination follow these associations up, down and across, the system is designed to also be followed by automated algorithms that could traverse this web quickly and efficiently.
So you can now see that a crystal structure held in the CSD could be the starting point for a journey of FAIR data discovery, in manner that has not hitherto been possible. How quickly the CSD will become populated by links to Raw (and other) data remains to be seen. I have not yet discovered any mechanism for specifying a CSD query which stipulates that Raw data must be available, but no doubt this will come.
To end, back to the Biomimetic Activation of CO2 referred to at the start. With no access to the original data, recourse was made to computational modelling.[2] Which where I came in, since I wanted access to the original (computational) data. Sadly it did not appear to be available with the article,[2] in much the same manner as the original complaint. Perhaps, when FAIR data becomes fully accepted as part of how science is done nowadays, such complaints will become ever rarer!
‡In fact the original authors did respond[4] with an acknowledgement that their original conclusions were not correct.
†Almost. The article [3] cites DOI: 10.14469/hpc/2099 (Ref 28), but it does not cite DOI: 10.5517/ccdc.csd.cc1n9ppb because the latter had not been minted yet at the time the final proofs were corrected, and there is no mechanism to add it at a later stage.
References
- S.L. Ackermann, D.J. Wolstenholme, C. Frazee, G. Deslongchamps, S.H.M. Riley, A. Decken, and G.S. McGrady, "Crystallographic Snapshot of an Arrested Intermediate in the Biomimetic Activation of CO<sub>2</sub>", Angewandte Chemie International Edition, vol. 54, pp. 164-168, 2014. https://doi.org/10.1002/anie.201407165
- J. Hurmalainen, M.A. Land, K.N. Robertson, C.J. Roberts, I.S. Morgan, H.M. Tuononen, and J.A.C. Clyburne, "Comment on “Crystallographic Snapshot of an Arrested Intermediate in the Biomimetic Activation of CO<sub>2</sub>”", Angewandte Chemie International Edition, vol. 54, pp. 7484-7487, 2015. https://doi.org/10.1002/anie.201411654
- J. Almond-Thynne, A.J.P. White, A. Polyzos, H.S. Rzepa, P.J. Parsons, and A.G.M. Barrett, "Synthesis and Reactions of Benzannulated Spiroaminals: Tetrahydrospirobiquinolines", ACS Omega, vol. 2, pp. 3241-3249, 2017. https://doi.org/10.1021/acsomega.7b00482
- S.L. Ackermann, D.J. Wolstenholme, C. Frazee, G. Deslongchamps, S.H.M. Riley, A. Decken, and G.S. McGrady, "Corrigendum: Crystallographic Snapshot of an Arrested Intermediate in the Biomimetic Activation of CO<sub>2</sub>", Angewandte Chemie International Edition, vol. 54, pp. 7470-7470, 2015. https://doi.org/10.1002/anie.201504197
Tags:computing, Context, data, Data management, Information, Knowledge, Raw data, software simulations, Technology/Internet
Posted in Chemical IT, crystal_structure_mining | No Comments »
Thursday, October 5th, 2017
We have heard a lot about OA or Open Access (of journal articles) in the last five years, often in association with the APC (Article Processing Charge) model of funding such OA availability. Rather less discussed is how the model of the peer review of these articles might also evolve into an Open environment. Here I muse about two experiences I had recently.
Organising the peer review of journal articles is often now seen as the single most important activity a journal publisher can undertake on behalf of the scientific community; the very reputation of the journal depends on this process being conducted responsibly, thoroughly and with integrity by the selected reviewers. Reviewers conduct this process voluntarily, mostly anonymously, without remuneration or recognition and often with short deadlines for completion. After one such process, I recently received an interesting follow-up email from the journal, suggesting I register my activity with Publons.com, a site set up to register and give non-anonymous credit for reviewing activities. I should say that Publons is a commercial company, set up in 2012 to to “address the static state of peer-reviewing practices in scholarly communication, with a view to encourage collaboration and speed up scientific development”. Worthy aims, but like many a .com company nowadays, one might ask what the back-story might be. Thus many of the Internet giants, Google, Facebook, Twitter etc, do have back-stories, which often underpin their business models, but which may only emerge years after their founding. With only a hazy idea of what Publons’ back-story might be, I went ahead and registered my reviewing activity. 
After doing so, I then accessed my entry. You only learn that I have reviewed for a particular journal, but nothing about the actual process itself. I did not really think that this experiment had done much to encourage collaboration and speed up scientific development. It might be useful for early career researchers to get their name exposed however.
I can almost understand why the review itself might not be publicly displayed, but as a result you learn nothing about the factual basis of the review and whether it might have been conducted responsibly, thoroughly and with integrity. Instead, I now suspect that the presence of my name on this site might merely encourage other publishers to deluge me with requests for further (freely donated) refereeing.
Discussing this at lunch, a colleague (thanks Ed!) reminded me of a veritable journal called Organic Syntheses. Here, authors submit a synthetic procedure and open identified “checkers” are invited to repeat the procedure and comment on it. The two roles are kept separate (i.e. the checkers do not become co-authors), but they could get credit for their activity. Thus if you view a typical recent entry[1] you will see a full biography and affiliation of the checkers given at the end, with footnotes often describing their own observations if they differ from those of the authors.
This set me thinking whether an open peer review process might also contain such an element of checking, as well as informed comment, nay opinion, about the article itself and the conclusions it makes. The opportunity arose when I was contacted by an author who was about to submit a computational article to a journal. This journal allowed open peer review. If I agreed to review, my name would be attached to the article if accepted for publication. I undertook this on the basis that I would use this review to conduct some limited checking of the computations and other assumptions underpinning the conclusions in the submitted article. I also wanted this open process to include the data on which my review was based. Most importantly if anyone wished to replicate my replication, the barriers to doing so should be as low as is possible. Shortly thereafter, I received a formal invitation from the journal and I set about my task. Crucially, all my own calculations supporting the review were archived in a data repository, albeit under embargo. In my cover letter I included the DOI for my data and the embargo access code, so that the authors (and the editor of the journal if they so wished) could inspect the data against which I wrote my review.
Then followed standard procedures, whereby the authors took my comments into consideration, revised the article and the final version was indeed accepted and published.[2] You will find the two referees/checkers listed, although unlike Organic Syntheses, there is no bibliographic information about them or their affiliation. I did ask the journal if they could at least link my ORCID identifier to my name, but that request was refused. If my name had been a common one, then disambiguating it into a unique identity could be a challenge. There was also no mechanism to associate my identity on the journal with any data on which I had based my review. Really, the only open aspect of this process was just my (potentially ambiguous) name, nothing else. No follow-up was received from the journal to add the review to Publons.
The next stage was to contact the author who had originally set the process under way to ask them if they would mind my releasing the data on which my review had been based. They agreed, as also they did to my telling this story. The overall outcome is thus a published article with the reviewers (if not their reviews or any supporting evidence for their review) openly named. In this specific case, there is also an open dataset with a formal link back to the article in the form of a DOI (10.14469/hpc/2640, although I suspect this aspect is unique, even precedent setting), but one driven by the reviewer and not the journal. It would be nice to have bidirectional links between both article and the review data, but I do not know any publishers currently operating such a mechanism (if anyone knows such, please tell).
Now to the broader questions about the process described above. I think that the aspiration to encourage collaboration and speed up scientific development may indeed have been promoted by this association between article and the data assembled by the reviewer. Whether the final article was improved as a result of the processes described here I will leave the authors to comment if they wish. As with the checkers employed by Organic Syntheses, such a review process takes not just time, but resources. Resources that currently have to be freely donated by the reviewers and their host institution and which clearly cannot become expensive, time-consuming or onerous. That was not the case as it happens here; my contributions were facilitated by my having sufficient expertise to perform the tasks I undertook really quite quickly.
I will raise one more issue; that of whether to add my review to the dataset which is now openly available. In fact it is not included, in part because it related to the initially submitted version of the MS. The final MS version has been revised and so many of the comments in my review may only make sense if you have the first version to hand. It would be perhaps unreasonable to make the first drafts of manuscripts routinely available (although historians of science would probably love that!) alongside the reviews of that first draft. But I could also see a case for doing so if the community agreed to it. One to discuss for the future I think. There is also the associated issue of what should happen to any dataset associated with a review in the event that the final article is rejected and not accepted. Should the data remain permanently under embargo and the reviewer’s identity permanently anonymous? Perhaps opening up even such datasets might nevertheless encourage collaboration and speed up scientific development, but I fancy some would consider that a step too far!
References
- J. Zhu, "Preparation of N-Trifluoromethylthiosaccharin: A Shelf-Stable Electrophilic Reagent for Trifluoromethylthiolation", Organic Syntheses, vol. 94, pp. 217-233, 2017. https://doi.org/10.15227/orgsyn.094.0217
- L. Li, M. Lei, Y. Xie, H.F. Schaefer, B. Chen, and R. Hoffmann, "Stabilizing a different cyclooctatetraene stereoisomer", Proceedings of the National Academy of Sciences, vol. 114, pp. 9803-9808, 2017. https://doi.org/10.1073/pnas.1709586114
Tags:Academic publishing, article processing charge, author, Company: Facebook, Company: Publons, Company: Twitter, editor, Electronic publishing, Entertainment/Culture, Hybrid open access journal, Internet giants, OA, Open access, Organic Syntheses, Public sphere, Publishing, Scholarly communication, search engines, Social Media & Networking, Technology/Internet
Posted in Chemical IT, General | 5 Comments »
Friday, June 2nd, 2017
In 2016, the world heard that gravitational waves had been detected and now a third instance is reported.‡ Given that the data associated with these detections are perhaps amongst the most important instances in recent times, I thought I might take a peek at how it was managed.
- The original report in 2016[1] cited (Ref 116) data as DOI: 10.7935/K5MW2F23.
- The second instance[2] also cites (Ref 89) a DOI: 10.7935/K5H41PBP
- Today† a third instance was reported[3] with data cited (Ref 180) as DOI: 10.7935/K53X84K2
- Sixth instance in 2017[4], Data (Ref 80) DOI: 10.7935/K5B8566F.
- A complete list of events is available at losc.ligo.org/events/
Each of these datasets is beautifully presented, with interactive components making the data very accessible and indeed FAIR. Recently, guidelines for how to cite data have emerged and the FORCE11 organisation has interpreted them for authors, publishers and journal editors, and repository administrators and it is good that the data for these detections has adhered to these principles. When implemented, it will identify e.g. Refs 116, 89 or 180 in the above articles with attributes that will trigger something called EventData with the objective that it retrieves and exposes the activity that occurs around research data objects and brings to light links between publications and data, citations, software, reuse, documentation, etc. At the moment I presume that these three data citations do not yet trigger any EventData. However, there are plans to for both CrossRef and DataCite to implement search procedures to find such EventData. When this service goes live, I intend to explore its potential; watch this space.
I did one other check on each of the datasets:
These download the metadata associated with each dataset. Ideally this could contain a host of information about the data and in particular its creators (i.e. the ORCID of each of the many authors describing how the data was acquired and interpreted). I show just the last as an example in full (the others are similar). Its pretty minimal.
Now there is an area that this otherwise magnificent example of open data sharing could improve upon. In a forthcoming post, I will show how rich metadata population of a chemistry dataset can be used to enhance it and also to trigger EventData as noted above.
‡For a famous chemical controversy involving gravitational fields, see here.
References
- B. Abbott, R. Abbott, T. Abbott, M. Abernathy, F. Acernese, K. Ackley, C. Adams, T. Adams, P. Addesso, R. Adhikari, V. Adya, C. Affeldt, M. Agathos, K. Agatsuma, N. Aggarwal, O. Aguiar, L. Aiello, A. Ain, P. Ajith, B. Allen, A. Allocca, P. Altin, S. Anderson, W. Anderson, K. Arai, M. Arain, M. Araya, C. Arceneaux, J. Areeda, N. Arnaud, K. Arun, S. Ascenzi, G. Ashton, M. Ast, S. Aston, P. Astone, P. Aufmuth, C. Aulbert, S. Babak, P. Bacon, M. Bader, P. Baker, F. Baldaccini, G. Ballardin, S. Ballmer, J. Barayoga, S. Barclay, B. Barish, D. Barker, F. Barone, B. Barr, L. Barsotti, M. Barsuglia, D. Barta, J. Bartlett, M. Barton, I. Bartos, R. Bassiri, A. Basti, J. Batch, C. Baune, V. Bavigadda, M. Bazzan, B. Behnke, M. Bejger, C. Belczynski, A. Bell, C. Bell, B. Berger, J. Bergman, G. Bergmann, C. Berry, D. Bersanetti, A. Bertolini, J. Betzwieser, S. Bhagwat, R. Bhandare, I. Bilenko, G. Billingsley, J. Birch, I.A. Birney, O. Birnholtz, S. Biscans, A. Bisht, M. Bitossi, C. Biwer, M. Bizouard, J. Blackburn, C. Blair, D. Blair, R. Blair, S. Bloemen, O. Bock, T. Bodiya, M. Boer, G. Bogaert, C. Bogan, A. Bohe, P. Bojtos, C. Bond, F. Bondu, R. Bonnand, B. Boom, R. Bork, V. Boschi, S. Bose, Y. Bouffanais, A. Bozzi, C. Bradaschia, P. Brady, V. Braginsky, M. Branchesi, J. Brau, T. Briant, A. Brillet, M. Brinkmann, V. Brisson, P. Brockill, A. Brooks, D. Brown, D. Brown, N. Brown, C. Buchanan, A. Buikema, T. Bulik, H. Bulten, A. Buonanno, D. Buskulic, C. Buy, R. Byer, M. Cabero, L. Cadonati, G. Cagnoli, C. Cahillane, J.C. Bustillo, T. Callister, E. Calloni, J. Camp, K. Cannon, J. Cao, C. Capano, E. Capocasa, F. Carbognani, S. Caride, J.C. Diaz, C. Casentini, S. Caudill, M. Cavaglià, F. Cavalier, R. Cavalieri, G. Cella, C. Cepeda, L.C. Baiardi, G. Cerretani, E. Cesarini, R. Chakraborty, T. Chalermsongsak, S. Chamberlin, M. Chan, S. Chao, P. Charlton, E. Chassande-Mottin, H. Chen, Y. Chen, C. Cheng, A. Chincarini, A. Chiummo, H. Cho, M. Cho, J. Chow, N. Christensen, Q. Chu, S. Chua, S. Chung, G. Ciani, F. Clara, J. Clark, F. Cleva, E. Coccia, P. Cohadon, A. Colla, C. Collette, L. Cominsky, M. Constancio, A. Conte, L. Conti, D. Cook, T. Corbitt, N. Cornish, A. Corsi, S. Cortese, C. Costa, M. Coughlin, S. Coughlin, J. Coulon, S. Countryman, P. Couvares, E. Cowan, D. Coward, M. Cowart, D. Coyne, R. Coyne, K. Craig, J. Creighton, T. Creighton, J. Cripe, S. Crowder, A. Cruise, A. Cumming, L. Cunningham, E. Cuoco, T.D. Canton, S. Danilishin, S. D’Antonio, K. Danzmann, N. Darman, C. Da Silva Costa, V. Dattilo, I. Dave, H. Daveloza, M. Davier, G. Davies, E. Daw, R. Day, S. De, D. DeBra, G. Debreczeni, J. Degallaix, M. De Laurentis, S. Deléglise, W. Del Pozzo, T. Denker, T. Dent, H. Dereli, V. Dergachev, R. DeRosa, R. De Rosa, R. DeSalvo, S. Dhurandhar, M. Díaz, L. Di Fiore, M. Di Giovanni, A. Di Lieto, S. Di Pace, I. Di Palma, A. Di Virgilio, G. Dojcinoski, V. Dolique, F. Donovan, K. Dooley, S. Doravari, R. Douglas, T. Downes, M. Drago, R. Drever, J. Driggers, Z. Du, M. Ducrot, S. Dwyer, T. Edo, M. Edwards, A. Effler, H. Eggenstein, P. Ehrens, J. Eichholz, S. Eikenberry, W. Engels, R. Essick, T. Etzel, M. Evans, T. Evans, R. Everett, M. Factourovich, V. Fafone, H. Fair, S. Fairhurst, X. Fan, Q. Fang, S. Farinon, B. Farr, W. Farr, M. Favata, M. Fays, H. Fehrmann, M. Fejer, D. Feldbaum, I. Ferrante, E. Ferreira, F. Ferrini, F. Fidecaro, L. Finn, I. Fiori, D. Fiorucci, R. Fisher, R. Flaminio, M. Fletcher, H. Fong, J. Fournier, S. Franco, S. Frasca, F. Frasconi, M. Frede, Z. Frei, A. Freise, R. Frey, V. Frey, T. Fricke, P. Fritschel, V. Frolov, P. Fulda, M. Fyffe, H. Gabbard, J. Gair, L. Gammaitoni, S. Gaonkar, F. Garufi, A. Gatto, G. Gaur, N. Gehrels, G. Gemme, B. Gendre, E. Genin, A. Gennai, J. George, L. Gergely, V. Germain, A. Ghosh, A. Ghosh, S. Ghosh, J. Giaime, K. Giardina, A. Giazotto, K. Gill, A. Glaefke, J. Gleason, E. Goetz, R. Goetz, L. Gondan, G. González, J.G. Castro, A. Gopakumar, N. Gordon, M. Gorodetsky, S. Gossan, M. 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Tags:Astronomy, Binary stars, Black holes, famous chemical controversy, General relativity, Gravitational wave, Gravity, Physics, search procedures, Technology/Internet, Wave
Posted in Chemical IT | 1 Comment »
Friday, June 2nd, 2017
In 2016, the world heard that gravitational waves had been detected and now a third instance is reported.‡ Given that the data associated with these detections are perhaps amongst the most important instances in recent times, I thought I might take a peek at how it was managed.
- The original report in 2016[1] cited (Ref 116) data as DOI: 10.7935/K5MW2F23.
- The second instance[2] also cites (Ref 89) a DOI: 10.7935/K5H41PBP
- Today a third instance was reported[3] with data cited (Ref 180) as DOI: 10.7935/K53X84K2
Each of these datasets is beautifully presented, with interactive components making the data very accessible and indeed FAIR. Recently, guidelines for how to cite data have emerged and the FORCE11 organisation has interpreted them for authors, publishers and journal editors, and repository administrators and it is good that the data for these detections has adhered to these principles. When implemented, it will identify e.g. Refs 116, 89 or 180 in the above articles with attributes that will trigger something called EventData with the objective that it retrieves and exposes the activity that occurs around research data objects and brings to light links between publications and data, citations, software, reuse, documentation, etc. At the moment I presume that these three data citations do not yet trigger any EventData. However, there are plans to for both CrossRef and DataCite to implement search procedures to find such EventData. When this service goes live, I intend to explore its potential; watch this space.
I did one other check on each of the datasets:
These download the metadata associated with each dataset. Ideally this could contain a host of information about the data and in particular its creators (i.e. the ORCID of each of the many authors describing how the data was acquired and interpreted). I show just the last as an example in full (the others are similar). Its pretty minimal.
Now there is an area that this otherwise magnificent example of open data sharing could improve upon. In a forthcoming post, I will show how rich metadata population of a chemistry dataset can be used to enhance it and also to trigger EventData as noted above.
‡For a famous chemical controversy involving gravitational fields, see here.
References
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Yancey, M. Yap, H. Yu, H. Yu, M. Yvert, A. Zadrożny, M. Zanolin, T. Zelenova, J. Zendri, M. Zevin, L. Zhang, M. Zhang, T. Zhang, Y. Zhang, C. Zhao, M. Zhou, Z. Zhou, X. Zhu, A. Zimmerman, M. Zucker, J. Zweizig, and . , "GW170104: Observation of a 50-Solar-Mass Binary Black Hole Coalescence at Redshift 0.2", Physical Review Letters, vol. 118, 2017. https://doi.org/10.1103/physrevlett.118.221101
Tags:Astronomy, Binary stars, Black holes, famous chemical controversy, General relativity, Gravitational wave, Gravity, Physics, search procedures, Technology/Internet, Wave
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Monday, May 29th, 2017
As the Internet and its Web-components age, so early pages start to decay as technology moves on. A few posts ago, I talked about the maintenance of a relatively simple page first hosted some 21 years ago. In my notes on the curation, I wrote the phrase “Less successful was the attempt to include buttons which could be used to annotate the structures with highlights. These buttons no longer work and will have to be entirely replaced in the future at some stage.” Well, that time has now come, for a rather more crucial page associated with a journal article published more recently in 2009.[1]
The story started a few days ago when I was contacted by the learned society publisher of that article, noting they were “just checking our updated HTML view and wanted to test some of our old exceptions“. I should perhaps explain what this refers to. The standard journal production procedures involve receiving a Word document from authors and turning that into XML markup for the internal production processes. For some years now, I have found such passive (i.e. printable only) Word content unsatisfactory for expressing what is now called FAIR (Findable, accessible, inter-operable and re-usable) data. Instead, I would create another XML expression (using HTML), which I described as Interactive Tables and then ask the publisher to host it and add that as a further link to the final published article. I have found that learned society publishers have not been unwilling to create an “exception” to their standard production workflows (the purely commercial publishers rather less so!). That exceptional link is http://www.rsc.org/suppdata/cp/b8/b810301a/Table/Table1.html but it has now “fallen foul of the java deprecation“.
Back in 2008 when the table was first created, I used the Java-based Jmol program to add the interactive component. That page, when loaded, now responds with the message:
This I must emphasise is nothing to do with the publisher, it is the Jmol certificate that has been revoked. That of itself requires explanation. Java is a powerful language which needs to be “sandboxed” to ensure system safety. But commands can be created which can access local file stores and write files out there (including potentially dangerous ones). So it started to become the practise to sign the Java code with the developer certificate to ensure provenance for the code. These certificates are time-expired and around 2015 the time came to renew it. Normally, when such a certificate is renewed, the old one is allowed to continue operation. On this occasion the agency renewing the certificate did not do this but revoked the old one instead (Certificate has been revoked, reason: CESSATION_OF_OPERATION, revocation date: Thu Oct 15 23:11:18 BST 2015). So all instances of Jmol with the old certificate now give the above error message.
The solution in this case is easy; the old Jmol code (as JmolAppletSigned.jar) is simply replaced with the new version for which the certificate is again valid. But simply doing that alone would merely have postponed the problem; Java is now indeed deprecated for many publishers, which is a warning that it will be prohibited at some stage in the future.‡ So time to bite the bullet and remove the dependency on Java-Jmol, replacing it with JSmol which uses only JavaScript.
Changing published content is in general not allowed; one instead must publish a corrigendum. But in this instance, it is not the content that needs changing but the style of its presentation (following the principle of the Web of a clear-cut separation of style and content). So I set out to update the style of presentation, but I was keen to document the procedures used. I did this by commenting out non-functional parts of the style components of my original HTML document (as <!– comment –>) and adding new ones. I describe the changes I made below.
- The old HTML contained the following initialisation code: jmolInitialize(".","JmolAppletSigned.jar");jmolSetLogLevel('0'); which was commented out.
- New scripts to initialize instead JSmol were added, such as:
<script src="JSmol.min.js" type="text/javascript"> </script>
- I added further scripts to set up controls to add interactivity.
- The now deprecated buttons had been invoked using a Jmol instance: jmolButton('load "7-c2-h-020.jvxl";isosurface "" opaque; zoom 120;',"rho(r) H")
- which was replaced by the JSmol equivalent, but this time to produce a hyperlink rather than a button (to allow the greek ρ to appear, which it could not on a button): <a href="javascript:show_jmol_window();Jmol.script(jmolApplet0,'load 7-c2-020.jvxl;isosurface "" translucent;spin 3;')">ρ(r)</a>,
- Some more changes were made to another component of the table, the links to the data repository. Originally, these quoted a form of persistent identifier known as a Handle; 10042/to-800. Since the data was deposited in 2008, the data repository has licensed further functionality to add DataCite DOIs to each entry. For this entry, 10.14469/ch/775. Why? Well, the original Handle registration had very little (chemically) useful registered metadata, whereas DataCite allows far richer content. So an extra column was added to the table to indicate these alternate identifiers for the data.
- We are now at the stage of preparing to replace the Java applet at the publishers site with the Javascript version, along with the amended HTML file. The above link, as I write this post, still invokes the old Java, but hopefully it will shortly change to function again as a fully interactive table.
- I should say that the whole process, including finding a solution and implementing it took 3-4 hours work, of which the major part was the analysis rather than its implementation.
It might be interesting to speculate how long the curated table will last before it too needs further curation. There are some specifics in the files which might be a cause for worry, namely the so-called JVXL isosurfaces which are displayed. These are currently only supported by Jmol/JSmol. They were originally deployed because iso-surfaces tend to be quite large datafiles and JVXL used a remarkably efficient compression algorithm (“marching cubes”) which reduces their size ten-fold or more. Should JSmol itself become non-operational at some time in the (hopefully) far future (which we take to be ~10 years!) then a replacement for the display of JVXL will need to be found. But the chances are that the table itself will decay “gracefully”, with the HTML components likely to outlive most of the other features. The data repository quoted above has itself now been available for ~12 years and it too is expected to survive in some form for perhaps another 10. Beyond that period, no-one really knows what will still remain.
You may well ask why the traditional journal model of using paper to print articles and which has survived some 350 years now, is being replaced by one which struggles to survive 10 years without expensive curation. Obviously, a 3D interactive display is not possible on paper. But one also hears that publishers are increasingly dropping printed versions entirely. One presumes that the XML content will be assiduously preserved, but re-working (transforming, as in XSLT) any particular flavour of XML into another publishers systems is also likely to be expensive. Perhaps in the future the preservation of 100% of all currently published journals will indeed become too expensive and we might see some of the less important ones vanishing for ever?†
‡Nowadays it is necessary to configure your system or Web browser to allow even signed valid Java applets to operate. Thus in the Safari browser (which still allows Java to operate, other popular browsers such as Chrome and Firefox have recently removed this ability), one has to go to preferences/security/plugin-settings/Java, enter the URL of the site hosting the applet and set it to either “ask” (when a prompt will always appear asking if you want to accept the applet) or “on” when it will always do so. How much longer this option will remain in this browser is uncertain.
†In the area of chemistry, an early pioneer was the Internet Journal of Chemistry, where the presentation of the content took full advantage of Web-technologies and was on-line only. It no longer operates and the articles it hosted are gone.
References
- H.S. Rzepa, "Wormholes in chemical space connecting torus knot and torus link π-electron density topologies", Phys. Chem. Chem. Phys., vol. 11, pp. 1340-1345, 2009. https://doi.org/10.1039/b810301a
Tags:Applet, compression algorithm, computing, Cross-platform software, HTML, HTML element, Internet Journal, Java, Java applet, Java platform, jmol, Markup languages, Open formats, publishers site, publishers systems, technology moves, Technology/Internet, the Internet Journal, Web browser, web technologies, Web-components age, XML, XSLT
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Thursday, May 25th, 2017
It is a sign of the times that one travels to a conference well-connected. By which I mean email is on a constant drip-feed, with venue organisers ensuring each delegate receives their WiFi password even before their room key. So whilst I was at a conference espousing the benefits of open science, a nice example of open collaboration was initiated as a result of a received email.‡
Steven Kirk 
contacted me with the following query: Do you know of any open-access database of calculated IRCs with coverage of as broad a range of classes of chemical reactions as possible? I recollected that about six years ago, I was exploring the use of iTunesU as a system for delivering course content in a rich-media format. I produced animations for about 115 reactions (many of which as it happens were taken from this blog, but quite a number were also unique to that project) and placed them into iTunesU, and now sending the URL https://itunes.apple.com/gb/course/id562191342 to Steven.
I should at this point explain something of the structure of such an iTunesU course.
- An essential feature is the course icon, seen below on the left. Since the course is hosted by Imperial College, it had to be an officially approved icon. I am sure you can believe me if I tell you that this took a month or so to obtain, with a fair bit of persistence required!
- I also had to get approval to place the iTunes app on all the teaching computers so that students could open the course. Believe me again when I tell you that I had to persuade the Apple lawyers in Cupertino to release a special license for this app to persuade our administrators here to install it on the Windows teaching clusters. Another few months had passed by.
- When creating an entry (using e.g. https://itunesu.itunes.apple.com/coursemanager/ ) one has to specify values for various descriptors, also often called metadata. Thus any one entry has fields for name and description, with the popularity added by Apple. Only a few words are visible in the description field, which can be expanded in iTunes using the i button.
- Steven meanwhile had replied asking if the original data that was used to generate the IRC might be available. Specifically his second question was “So the DOIs are only stamped into the animation’s bitmaps, or are they also somewhere in the metadata?“. That little i button is not easy to spot, and there is no indication, in the event, of what information it might actually contain.
- Here it is expanded. The contents are unstructured text, into which I have placed the required DOI.
- The lesson here is that I had fortunately had the foresight to include a link to the IRC data in anticipation of just such a question from someone in the future. But black mark to Apple here; the text cannot be selected and copied into a clipboard! It is fairly unFAIR data, since it can only be inter-operated (the I of FAIR) by a human re-typing it by hand. And the human has also to recognise the pattern of a DOI; a machine could not obtain this information easily. Moreover Steven is a Linux user; he does not readily have access to the iTunes app on this operating system!
- Also, there were 115 such entries, and now the prospect was rearing that each would have to be hand processed. Moreover, because the text was unstructured, there was no guarantee that I would have adopted the same pattern for all 115 entries.
- Fortunately Steven was on the ball. I quote again: it turns out iTunes isn’t needed at all. A service I found on the web http://picklemonkey.net/feedflipper-home/ takes an ITunes URL and converts it to an RSS feed. Opening this feed in Firefox and RSSOwl respectively let me save the feed as XML and HTML (both attached).
- This is currently where we stand (Steven’s first email was two days ago), but it’s not finished yet. Depending on how assiduous I was five years ago, some DOIs to the data may be acquired from the list. Sometimes I simply wrote e.g. See http://www.ch.imperial.ac.uk/rzepa/blog/?p=6816 knowing that the links to the data were there instead. I can already see that some descriptions have neither a DOI nor a link to the blog. More detective work will be needed, unfortunately.
How might the situation described above been avoided? Well, Apple in iTunesU only provided in effect one metadata field, and this was an unstructured one. Anything went in that field. Had they provided (or had the course creator been able to configure it themselves) there might have been another field entitled say “data source“. This could moreover been made a mandatory field and a structured one. Thus it might have only accepted known types of persistent identifier, such as a DOI. Further, the system could have checked that the DOI was actually resolvable. Before you ask, I did log a “bug” with Apple asking this be done, but nothing ever was. With such a tool to hand, I might have achieved data sources for all the 115 entries. The resulting XML (as generated above) could have been used to automate the retrieval of all 115 datasets describing this course.
At this stage then, Steven can follow-up his interest in building a reaction IRC library and analysing it. I will do all I can to encourage Steven not to make the mistakes I did and to ensure that any further data that is required to augment the library does not suffer the problems above. On the other hand, I console myself that in two days, much of the data for the course I created five years ago was salvageable; I wonder how many other iTunesU courses there are for which that can be said!
I will let (with some blushing) the final word be Steven’s: You are one of the few chemists who has both pioneered and built the principles of ‘open chemistry’ into their actual scientific work. I visit your blog occasionally knowing that there is a very high probability I could download and tinker with the results of real calculations.
‡Might I assure all the speakers that I concentrated totally on their talks rather than incoming emails!
Tags:animation, chemical reactions, City: Cupertino, Company: Cupertino Elec, Company: Firefox Communic, Computer Hardware - NEC, computing, detective, Digital media, Drip, Electronic documents, Electronic publishing, Email, HTML, Imperial College, Linux, operating system, Password, Person Location, Steven Kirk, Technology/Internet, XML
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Tuesday, May 23rd, 2017
This is taking place in the idyllic surroundings of the Niederwald forest, Rüdesheim, Germany. Here I highlight only aspects of the first three talks.
Martin Hicks introduced the conference with concepts such as the global public good. In the area of open access, he reminded us of the terms Platinum/Diamond open access, which are journals with no article processing charges (which can reach £5000 per article for some other OA journals), but which go with the challenge of ensuring that more gatekeepers of this global public good are needed to avoid being overwhelmed. He ended by asking us all to consider what the unit of knowledge is that needs to be shared.
The first talk was by Klaus Tochtermann who (amongst other topics) brought to our attention the Dutch GoFAIR initiative in the European Open Science Cloud, sub-divided into Go-train (i.e. data experts, who will build e.g. metadata tools) and Go-build (eco-systems: Internet of FAIR data and FAIR services). I think the message is that all organisations with chemistry labs should consider this as being an essential part of their future infrastructures.
Jeremy Frey’s title was Reducing Uncertainty: The Raison d’Être for Open Science who defined the fundamental principles of open science as transparency, capability and obtainability and encouraged data publication at source (as opposed to e.g. PhD writing up period) to ensure fidelity in the capture of metadata.
The team of Leah McEwen, Ian Bruno, Stuart Chalk and Richard Kidd told us about Global Data Initiatives and Chemistry and the need for social and technical bridges to enable open data sharing. I learnt for example that the IUPAC Gold book of chemical terms and definitions now has DOIs for each of the terms. Thus chemical shift (DOI: 10.1351/goldbook.C01036[1]), spectroscopy (DOI: 10.1351/goldbook.S05848[2]) and electron density function (DOI: 10.1351/goldbook.ET07024[3]). I will now to associate such links with e.g. deposited NMR data to help increase the semantics of the data (see e.g. DOI: 10.14469/hpc/1975).
Finally, a photo from the region, taken from the gondola adjacent to the venue and riding down to the small town on the banks of the Rhine.
References
- "chemical shift", The IUPAC Compendium of Chemical Terminology, 2014. https://doi.org/10.1351/goldbook.c01036
- "spectroscopy", The IUPAC Compendium of Chemical Terminology, 2014. https://doi.org/10.1351/goldbook.s05848
- "electron density function", The IUPAC Compendium of Chemical Terminology, 2014. https://doi.org/10.1351/goldbook.et07024
Tags:article processing charges, Bad Kreuznach, chemical shift, chemical terms, City: Rüdesheim, Country: Germany, Hesse, Hesse-Nassau, Ian Bruno, Jeremy Frey, Klaus Tochtermann, Leah McEwen, Martin Hicks, metadata tools, Niederwald, Niederwalddenkmal, Quotation, Rheingau-Taunus-Kreis, Rhine, Richard Kidd, Rüdesheim, Rüdesheim am Rhein, Rüdesheim an der Nahe, spectroscopy, States of Germany, Stuart Chalk, Technology/Internet
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