The theme of the meeting was data, and this resulted in a wealth of presentations with cheminformatics. What is striking here is that a lot of work has not changed so much in 20 years, except for the scale. What I missed here was the large open data sets, but generally the level of open science was heartwarming! So many preprints mentions, GitHub repositories, and Zenodo deposits. The Blue Obelisk was truly ahead of its time, but it is a delight to see the field of chemistry catch up. I can now say a lot of about peer review, and why the field is not benefitting from all the experience that exists in the field because people publish in the wrong journals, but that is for another time.

I attended multiple sessions, which is a bit of a challenge, doing this remotely from Central European Summer Time (CEST). Of course, the Sunday started with the Chemical informatics (R)evolution: Towards Democratization and Open Science session, where I had my first talk, and later that day the Enhance your Data - Smart Ways to Metadata and Knowledge Graphs session, where I gave a second talk, about Bioschemas’ ChemicalSubstance and MolecularEntity. Sadly, I had to leave that meeting early because it was getting too late.

There were so many interesting sessions, I could not attend everything. I also have to go back to all my notes and isolate things I want to follow up on, prominently open datasets.

More later.

Graphs like this show information on how people are using my work, which in turn allows me to further support. But this relies on open citations.

In my opinion, citations are an essential part of our research process. It gives us access to import prior work on which a study is based, and reflects how a work influences other research or even is essential to that other work. For example, it allows us to not repeat earlier published work, while preserving the ability to reproduce the full work. The Initiative for Open Citations encourages these citations to be publicly available to benefit research, but removing barriers to access this critical part of scholarly communication. While many societies and publishers have joined this initiative, the American Chemical Society (ACS) has not yet. By not joining the limit the sharing of knowledge for unclear reasons.

And I would really like to see the ACS to join this initiative, and proposed this a few times already. Because they still have not joined the initiative, I have started this petition. If you agree, please sign and share it with others.

Because getting this information out in the open is important, I think it’s a good idea to add them to Wikidata (see doi:10.3897/rio.1.e7573). So, with Bioclipse (doi:10.1186/1471-2105-8-59) I redrew the structure:

I previously blogged about how to add chemicals to Wikidata , but I realized that I wanted to also use Bioclipse to automate this process a bit. So, I wrote this script to generated the SMILES, InChI, InChIKey, double check the compound is not already in Wikidata (using the Wikidata SPARQL endpoint), an look up the PubChem compound identifier (example SMILES).

smiles = "CCCC"

mol = cdk.fromSMILES(smiles)
ui.open(mol)

inchiObj = inchi.generate(mol)
inchiShort = inchiObj.value.substring(6)
key = inchiObj.key // key = "GDGXJFJBRMKYDL-FYWRMAATSA-N"

sparql = """
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
SELECT ?compound WHERE {
  ?compound wdt:P235 "$key" .
}
"""

if (bioclipse.isOnline()) {
  results = rdf.sparqlRemote(
    "https://query.wikidata.org/sparql", sparql
  )
  missing = results.rowCount == 0
} else {
  missing = true
}

formula = cdk.molecularFormula(mol)

// Create the Wikidata QuickStatement,
// see https://tools.wmflabs.org/wikidata-todo/quick_statements.php

item = "LAST" // set to Qxxxx if you need to append info,
              // e.g. item = "Q22579236"

pubchemLine = ""
if (bioclipse.isOnline()) {
  pcResults = pubchem.search(key)
  if (pcResults.size == 1) {
    cid = pcResults[0]
    pubchemLine = "$item\tP662\t\"$cid\""
  }
}

if (!missing) {
  println "===================="
  println "Already in Wikidata as " + results.get(1,"compound")
  println "===================="
} else {
  statement = """
    CREATE
    
    $item\tDen\t\"chemical compound\"
    $item\tP233\t\"$smiles\"
    $item\tP274\t\"$formula\"
    $item\tP234\t\"$inchiShort\"
    $item\tP235\t\"$key\"
    $pubchemLine
  """

  println "===================="
  println statement
  println "===================="
}

The output of this script is a QuickStatement for Magnus Manske’s tool (IMPORTANT: it’s not meant to automate editing Wikidata! I only automate creating the input, which I carefully check (e.g. checking all stereochemistry is defined)! Note, how Bioclipse opens up the structure in a viewer with ui.open()), which is a list of commands to create and edit entries in Wikidata. You need to enable it first, but if you have an account, this is not too hard. Of course, the advantage is that it is a lot quicker. I have similar script to create QuickStatements starting with only a ChEMBL identifier.

The QuickStatement for GDC-0853 looks like:

    CREATE
    
    LAST Den "chemical compound"
    LAST P233 "O=C1C(=CC(=CN1C)c2ccnc(c2CO)N4C(=O)c3cc5c(n3CC4)CC(C)(C)C5)Nc6ncc(cc6)N7CCN(C[C@@H]7C)C8COC8"
    LAST P274 "C37H44N8O4"
    LAST P234 "1S/C37H44N8O4/c1-23-18-42(27-21-49-22-27)9-10-43(23)26-5-6-33(39-17-26)40-30-13-25(19-41(4)35(30)47)28-7-8-38-34(29(28)20-46)45-12-11-44-31(36(45)48)14-24-15-37(2,3)16-32(24)44/h5-8,13-14,17,19,23,27,46H,9-12,15-16,18,20-22H2,1-4H3,(H,39,40)/t23-/m0/s1"
    LAST P235 "WNEODWDFDXWOLU-QHCPKHFHSA-N"
    LAST P662 "86567195"

The first line creates a new Wikidata item, while the next ones add information about this compound. GDC-0853 is now also Q23304817. The label I added manually afterwards. Note how the Bioclipse script found the PubChem identifier, using the InChIKey. I also use this approach to add compounds to Wikidata that we have in WikiPathways.

Look at what they suggest and think about it. Include SMILES strings for structures in the paper. I very much welcome this, of course, despite I am not a big fan of SMILES at all. They could have said something about OpenSMILES too, which is more precise. They do say something about the InChI and InChIKey, but not that the SMILES string can more precisely reflect the drawing. I wonder why they don’t go for a format that can actually capture the image, like CML or a MDL molfile. Then again, a SMILES copy/pastes so nicely. Talking about slow innovation. There is zero technical reason you could not copy/paste a MDL molfile into a spreadsheet (and you can with many tools, in fact…)

Now, I still have tons of questions. What tool will be used to validate the correctness and absence of ambiguity before the publication? Will the SMILES strings be validated at all? And at what level? Will it have to be compatible with particular tools? Does it have to be compatible with OpenSMILES? Under what license will these SMILES be available (can we data mine DOI-SMILES links and openly share them)? What was the reasoning for finally adopting this? Will the journal also accept submission where both SMILES and other formats are provided? Will they accept or deny SMARTS strings (e.g. for Markush structures)?

All in all, I second the others, and am happy to see this step. I do hope they do not stop here and wait again 15 years for another step. In fact, they ask for input on jmc@jmedchem.acs.org. That is double promising!

The feed for Chemical Biology shows 79 feed items and the first one was a Environ. Sci. Technol. paper. The first of the 108 papers listed in the feed for Molecular Pharmaceutics is a perp from J.Phys.Chem.C.

Akregator is the RSS client that I use, and I noticed the exact same problem ES noted: every now and then, twice, three times a month, the RSS feeds for one journal give the content of another journal. For example, I get the TOC of Chemical Reviews in the RSS feed of the JCIM. Things like that.

Now, because Akregator has absolute nothing to do with Google, it cannot be Google who is messing up the RSS feeds. Because ES is having the same issues I have, it cannot be Akregator either. Ergo, it is the RSS feed system of the ACS itself that is messed up.

The GSoC

Now that I am talking about the GSoC, you might have realized that the CDK and Bioclipse did not make it as mentoring organization. While I had not seriously expected it, all the enthusiasm from within both projects including several interested students, I was a bit hoping for getting accepted with at least on of them. Meanwhile, KDE, as expected, is approved, and actually contains two interesting chemistry project ideas too. One is about a 3D viewer/editor for which 7 students send Google a proposal, and the other about text mining of chemical content on the desktop, using Strigi (two students). Both topics have one excellent proposal, who do good in the ranking process. So, we might have some chemistry in the GSoC after all.

CINF

OK, back to the ACS meeting. Fahrenbach had a presentation on blogging too, but don’t remember anything special about it. The CHED session was more elaborate on the whole topic, and since you are a reader of chemical blogs, you all know about this anyway :) Loney introduced biotechexchange.org which is building a social network around biotechnology. There are other community sites like this, and my major problem with these community building efforts is that they are too well defined. I much prefer to work in a more open environment where I can get in contact just as easily with people outside some specific topic. For the rest, the set of technologies is rather comprehensive.

Frenkel spoke about the imminent success of ThermoML, which is now being supported by vendors and publishers, smoothing the whole dissemination of data supported by this format. It is basically what CML is attempting to achieve in molecular structure data. Day is having a good go at this with crystal data, and his CrystalEye project is supposed to be launched next month.

Hey, at Microsoft.com, had a rather manager level presentation, with very little value for someone into the field of ‘data lifecycle and curation’. Rather disappointing on a scientific conference, or am I judging the ACS conference here? If the Microsoft is getting interested in chemoinformatics that might be a good thing, as long as the are OK with open source, open data and open standards. Who knows…

Rzepa had his presentation on the semantic wiki, which he, in similar form, held at the German Chemoinformatics Conference too . New, I think, were the sheets on reasoning based on the content of the wiki. That was rather interesting. If we all would make our chemical knowledge available as RDF, then this can become a big thing very soon. I skipped the presentation of Renear on ontologies, though it was actually one that I had hand picked; but I was simply too tired. Will watch the podcast when available. (BTW, are they making podcasts for the CINF session only, or for the whole ACS meeting?)

In the afternoon, I also followed just a subset of the presentations. The last one was by Scott who spoke earlier on Second Life . I’m really interested in seeing where this is going, though I have my reservations if this is the right medium for mining chemical knowledge. Today she spoke on the social bookmarking and podcasting initiatives at Nature and Nature Network. The latter is a social site, like like BioTechExchange, but not limited to one specific topic, and more interdisciplinary (my account at NN). I blogged about some early issues some time ago.

Jmol

Jabri showed us how Jmol is adding value to the ACS Chemical Biology journal. Yes, that’s what she said. An opensource tool, developed by people on their free time, is making an ACS journal more valuable. I am very happy to hear that, and it strongly supports our view that opensource chemoinformatics is very important. Some more support from established organizations might be in order indeed!

Blue Obelisk

It has become a habit to organize Blue Obelisk dinner to talk about opensource, opendata, openscience, and the future. Actually, we secretly talk about talking over the world, but I can’t say that. (Neither can I tell anything about our secret rituals. The protocol for becoming member of our society is quite simple though: be clear about your opinion that ODOSOS is the future.) Dinner was great, and it was great talking to several older and newer members of the movement. Cheers all! Oh, there also was some awards involved, but I hope Peter and Christoph will blog about that and post the pictures.

CINF morning

Yeah, more CINF session reports; I’m a chemoinformatician, remember. Chen showed us around in the latest changes in ChemDB, such as retrosynthesis planning. Banik shows a patented method for showing differences in a set of spectra, though his examples were not really impressive; if the method is really powerful, the examples might have been picked a bit more careful. And I have to say, in retrospect, I found the presentations in the CINF sessions typically of lower quality than I had expected for the big ACS meeting. Fortunately, meeting all the people here makes more than up for that. Guha presented a potentially powerful method to cluster large and huge data sets with a method that approximated SVD by splitting up the full matrices into many smaller ones.

Laptop Lane

The idea was that us bloggers met up, but that did not quite work out. No problem though. Spoke about many things with several people. Peter pointed me to an email from Noel on getting blog comments on JACS/ChemComm/JCIM papers on the table of contents. And somewhere that day, Jean-Claude pointed me to more chemistry in Second Life (set up by Beth). Both are great follow ups on the blog/wiki session by CHED yesterday ! Around 17:00 we left for one of the receptions in the W hotel in one of the WOW rooms, though the view was not that spectacular:

Bulls

I did not stay very long at the party, as I had to leave for the Bulls game against Portland. That was fun indeed! If I knew my first breakfast was going to cost 22 dollar, I would have bought a better ticket, but now I had a Stand 1 ticket which is so high up in the stadium that even the security people had not idea where to send me :) The view was still more than good enough to feel the pain/joy of the blocks and dunks-in-your-face:

My first day at the conference was interesting. The huge facility makes navigation a bit problematic, and we seemed to make it a habit to explore the wrong end of the building before heading in the right direction. There are a lot of maps in the ACS On-Site Meeting Program, but a nice overview map is lacking. Anyway, I spent the morning session in the ‘blog, wiki, and podcast session’, and the afternoon in CINF session honoring Prof. Wiggins.

CHED

Vogel was the first speaker in the CHED C Section morning session, and spoke about blogs and RSS feeds in general. Mitch’ Yahoo Pipes hackup was mentioned in one of the talks in this morning session. Currano followed with a discussion on social bookmarking, and so did Pence who focussed on the function in education. Francl put chemical blogging in some perspective which led to a short discussion on the difference in idea between blogs and wiki’s. Gelder and Picione spoke about podcasting as multimedia blogs. Scott represented recent work by Nature in exploring Second Life technologies, and mentioned the chemistry on their island, which happened to host a session of the First Online EMBL PhD Symposium last year . Bradley spoke about how he integrated blogs and wiki’s into there practicals. The atmosphere of the session was relaxed and the discussion lively.

CINF

The downside of all these parallel sessions is that it is bound to give clashes. It’s apparently even supposed to, because the ACS website private schedule assistant is made to make you aware and resolve such clashes. So, while I had to skip the CINF morning session honoring Wiggens, I had to skip the CHED session on social networking continuing on the CHED morning session. For example, I has to miss the presentation by Rzepa on the semantic wiki (Henry, I hope to have made up for it, by plugging your work here :)

Murray-Rust was the first speaker of the CINF Section A afternoon session, and talked about mashups, text mining and other things done in Cambridge. He also mentioned recent Greasemonkey scripts using comments from and enhancing our chemical blogs, now described at the Blue Obelisk website. (Especially the Chemical blogspace enhanced TOC of chemistry journals is nice.) Wild spoke about integrating text mining and chemoinformatics tools, and showed a mockup of a ‘by the way’ system for PubChem, where a PubChem entry would be enhanced with ‘BTW, did you know that these 7 articles mention this molecules, and that … etc’. These things are going to happen this year. Heller held his usual talk on InChI and PubChem, though the content has slightly changed since the last two versions I’ve seen (not the message, though). Doman gave a practical example showing backing up earlier statements that too much information is lost in the publication process. Heritage showed Elsevier/MDL’s view on the future of chemoinformatics, and accurately touched where it is currently failing. Amusingly, he pointed out that Elsevier, the publisher, would love to see more accurate QSAR/QSPAR/VS/etc models; ironically, it is, actually, for a large part caused by data not ending up in publications that predictive models are not as accurate as they could be. So, while looking at the chemoinformaticians/metricians, they should really be looking at themselves.

Some of these presentations mentioned directly or indirectly things I worked on. Thanx for doing that! Because I knew that there was funding for going to this meeting, only after the poster submission deadline was closed, I am not in the opportunity to present my work myself.

The evening is for the traditionally parties, time to eat, drink, network, make deals and try to convince others about the virtues of ODOSOS .

A last reminder: tomorrow afternoon at 13:00 at Laptop Lane in the exposition area is a meeting of chemical bloggers. Please join and chat IRL for once! :)

There were several other Dutch chemists on the plane, among which a few formed postdocs from Nijmegen, who I knew from the time I was still a M.Sc. student in organic chemistry. The plane was nice too, a Boeing 747, the first time I flew with one. OK, there now is the new Airbus, so the Boeing has lost some of its prestige, but here’s the image anyway:

The 380 is actually supposed to be in Chicago, but I did not see it. OK, going for breakfast now, and to the ACS conference site afterwards.