tag:blogger.com,1999:blog-17889588.post4402515701672420910..comments2024-03-13T07:14:55.283+01:00Comments on chem-bla-ics: Blogs I Follow: Henry RzepaEgon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.comBlogger9125tag:blogger.com,1999:blog-17889588.post-70899573967144560462012-02-05T14:37:39.883+01:002012-02-05T14:37:39.883+01:00Nice write up!Nice write up!Egon Willighagenhttps://www.blogger.com/profile/07470952136305035540noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-17970493712168016262011-11-04T12:31:28.006+01:002011-11-04T12:31:28.006+01:00You can read my take on a data-descriptor at www.c...You can read my take on a data-descriptor at <a href="http://www.ch.ic.ac.uk/rzepa/data-descriptors/" rel="nofollow">www.ch.ic.ac.uk/rzepa/data-descriptors/</a>.<br /><br />It is not meant as a data schema, but more of a human readable data life cycle, linked to a real example. It could of course expand (possibly uncontrollably), but I would hope it could induce other chemists who create and share data to write something similar, as a way of improving the profile of molecular data amongst researchers, and not just amongst cheminformaticians.Henry Rzepahttp://www.ch.ic.ac.uk/rzepa/blog/noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-83191083310679615272011-11-02T07:29:33.032+01:002011-11-02T07:29:33.032+01:00I'm looking forward to reading that!I'm looking forward to reading that!Egon Willighagenhttps://www.blogger.com/profile/07470952136305035540noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-37102908189182789222011-10-25T20:53:32.519+02:002011-10-25T20:53:32.519+02:00An article got half written once! But I have now b...An article got half written once! But I have now been asked by a forward looking publisher to write something called a <i>data descriptor</i> to help both prospective authors of research articles, and readers of journals, to understand the chemistry <i>data life cycle</i> better. Its almost finished, and it will be distributed under a CC 2.5 license. This contains something on the topic you allude to.Henry Rzepahttp://www.ch.ic.ac.uk/rzepa/blog/noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-83794134769934027222011-10-19T06:05:06.527+02:002011-10-19T06:05:06.527+02:00Ah, I did not know you had been using DSpace that ...Ah, I did not know you had been using DSpace that active! Did you ever write up how you've integrated it into your workflow? Particularly the HPC platform?Egon Willighagenhttps://www.blogger.com/profile/07470952136305035540noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-72153108445106980602011-10-18T23:08:41.778+02:002011-10-18T23:08:41.778+02:00The first point; citations for the Jmol visualisa...The first point; citations for the Jmol visualisations. Unfortunately, when Webcite archives a blog post, it does not replicate the Jmol functionality. That aspect of it is not active in the archive.<br /><br />Second point. We use Dspace, and have done so for 6 years (see <a href="http://dx.doi.org/10.1021/ci7004737" rel="nofollow">here</a>). Quixote is quite new. To my knowledge it does not have Handle functionality, and in effect cannot be resolved using the same mechanisms as a DOI. Dspace has many faults, but it has been stable for us over this period, and we now have some 10,000 deposits using it. In our case, the Dspace repository is actually linked to the batch queues for our high performance computing cluster, which means the two talk to each other very effectively.<br /><br />Third point. Dspace actually archives a whole collection of files. Thus <a href="http://dx.doi.org/10042/to-9509" rel="nofollow">see here</a> for the files. These include an RDF declaration of appropriate metadata in the form of a METS manifest. In the wget command I listed, replace the string "logfile.out" by any of the other files you might want to acquire. These include a CML file, and possibly other useful information.Henry Rzepahttp://www.ch.ic.ac.uk/rzepa/blog/noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-1362678743043679422011-10-17T12:46:59.066+02:002011-10-17T12:46:59.066+02:00Henry, I was more thinking about citations for the...Henry, I was more thinking about citations for the Jmol visualizations... but when you mention a repos for the calculations, you must be using Quixote, I guess... that would be a great combo and boost for Quixote!<br /><br />Maybe we should talk to Sam and ask him how a Quixote page can easily be embedded in blog posts :)<br /><br />Regarding the wget command... how would I learn what URL to use?Egon Willighagenhttps://www.blogger.com/profile/07470952136305035540noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-76546383542850471702011-10-12T13:50:23.747+02:002011-10-12T13:50:23.747+02:00Yes, the double Avatar is a bug! It seems to apply...Yes, the double Avatar is a bug! It seems to apply only to the latest post and seems to be due to the Chemicalize extension.<br /><br />As for permalinks, a small number of the posts are in fact permanently archived using WebCite; http://www.webcitation.org/ It would be nice to have a WordPress extension that could do this routinely, but no such exists. Unfortunately, WebCite does not of itself allocate a DOI handle to this.<br /><br />As for the downloads, there are two mechanisms, neither entirely ideal.<br /><br />I do try to quote a DOI handle for the digital repository entry for a calculation. This would in principle allow for the entry to be scrapped by a script. See <a href="http://www.ch.ic.ac.uk/rzepa/talks/acs11-cinf/5d.html" rel="nofollow">this slide</a> via something like:<br /><br />wget --quiet --no-check-certificate https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/to-$T/logfile.out -O to-$T.log; <br /><br />I also wrote <a href="http://www.ch.ic.ac.uk/rzepa/blog/?p=3154" rel="nofollow">this post</a> which describes how data can be extracted from a Jmol instance. But that method depends on a human; to my knowledge there is no way of scripting this to happen automatically. However, Bob Hanson has achieved miracles with scripting Jmol, and it might be possible.<br /><br />Clearly however, a mechanism for exposing better metadata declarations of the data contained in a blog post such that bots can acquire it without human intervention are needed. If they exist, do let me know!Henry Rzepahttp://www.ch.ic.ac.uk/rzepa/blog/noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-32729735503715283332011-10-12T00:18:24.722+02:002011-10-12T00:18:24.722+02:00"Denouement" is the technical term for t..."Denouement" is the technical term for the conclusion in classic dramatic structure. We learned that term in my high school English class in the US, and its use here seems more a literary than French allusion.Andrew Dalkehttps://www.blogger.com/profile/17091314849699854287noreply@blogger.com