Christoph Steinbeck | 26 May 17:23 2016
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Regarding liberated BO article in JCIM: Your PMC ID PMC4878861 for ACS article ci050400b

Dear all, 

please see below for your information.

Kind regards, Chris

--
Dr. Christoph Steinbeck, Head of Cheminformatics and Metabolism
European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory
Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Phone +44 1223 49 2640, Email: steinbeck@..., Admin: kholmes@...
https://www.ebi.ac.uk/about/people/christoph-steinbeck
http://orcid.org/0000-0001-6966-0814
> 
> 
> Dear Dr. Christoph Steinbeck,
> 
> ACS is pleased to share that your final published article:
> 
> The Blue ObelisksInteroperability in Chemical Informatics  ci050400b
> 
> has been successfully deposited for immediate availability after the date of first web publication to
PubMed Central (PMC) as part of ACS' Certified Deposit program, one of the benefits of choosing an ACS
AuthorChoice option.
> 
> The article has been assigned 
> 
> PMCID# PMC4878861  
> 
> This ID number can now be used for grant reporting purposes. You are also encouraged to forward this PMCID
(Continue reading)

Egon Willighagen | 28 Mar 14:58 2016
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soon: BODR 11 release

Hi all,

thanks to work by others, it is time for a BODR 11 release (should
have been earlier)... the changelog is given below.

I will make the release on April 27... and this email is a last call
for updates: if you want to do some work, do it soon.

The source code is on GitHub: https://github.com/egonw/bodr

Grtz,

Egon

2016-03-28 Egon Willighagen <egon.willighagen@...>
* elements/symbols.bibxml: added two references for recently confirmed elements

2014-10-09 vaitkus <antanas.vaitkus90@...>
* elements/elements.xml: fixed the element symbol for Lv
* elements/elements.xml: added missing group information

2014-10-07 vaitkus <antanas.vaitkus90@...>
* elements/elements.xml: updated group information

2014-02-20 Bert de Jong <wadejong@...>
* elements/elements.xml|radii-covalent.xml: update covalent radii per
Pyykko 2009

--

-- 
E.L. Willighagen
(Continue reading)

Robert Hanson | 9 Mar 03:33 2016

great InChI JavaScript library

Whom do we have to thank for this? Noel?

Bob



--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

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Peter Murray-Rust | 8 Mar 19:43 2016
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List of chemical names and identifiers

I am now enhancing contentmine.org to search the daily literature and need dictionaries to match names. I don't mind false negatives so am simply matching names, but they should have identifiers.

The format would simply be:
name="ethyl acetate" id="a123"

Peter Ertl has supplied a list of > 10000 wikipedia entries + Inchis (thanks).

I would ideally like classifications such as:
drugs (INNs)
pesticides
herbicides
etc.
as that will help to get non chemists interested.

The size of dictionaries can be between 100 and 100K approx.

Is there a simple way to get such a list out of ChEBI?

P.


--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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Robert Hanson | 7 Mar 20:20 2016

Question about JavaScript implementation of InChI generation

Richard, I have a question about the JavaScript implementation of InChI creation. Are you the person to ask?

I have that working now at http://chemapps.stolaf.edu/jmol/jsmol/inchi.htm, and I see excellent agreement with NCI/CADD.

But there is a problem. When trying a variety of options, I stumbled upon this oddity trying this particular sequence:

[load page]
morphine

- no problem

[load page]
taxol
methanol

- no problem

[load page]
taxol
methanol
morphine

- inchi.js seems to have crashed or is looping or something. Morphine call does not return, and no further processing of other molecules works.


[load page]
taxol
morphine

- same issue.

So it appears that taxol is pathological in that it sets something up such that a later request for morphine fails. The taxol model from NCI/CADD is worthless because it is a flat 2D model. inchi.js does return something:

InChI=1S/C47H51NO14/c1-25-31(60-43(56)36(52)35(28-16-10-7-11-17-28)48-41(54)29-18-12-8-13-19-29)23-47(57)40(61-42(55)30-20-14-9-15-21-30)38-45(6,32(51)22-33-46(38,24-58-33)62-27(3)50)39(53)37(59-26(2)49)34(25)44(47,4)5/h7-21,31-33,35-38,40,51-52,57H,22-24H2,1-6H3,(H,48,54) Omitted undefined stereo

but then after that it seems dead in the water specifically for morphine. The call is made, no error is reported, and no further calls can be made.

Any way to debug this?

Bob

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Peter Murray-Rust | 7 Mar 14:56 2016
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ContentMining of chemical facts


In contentmine.org we are close to being able to extract Open facts from the literature on a daily basis.  We intend to do all journals, including closed access, but have started with Open to develop the technology. To test this we are searching EuropePubMedCentral for facts such as sequences, genes, species, etc. See https://www.youtube.com/watch?v=5lYzOZ2Cv_I for a 5 minute video about Zika.

IT's relatively straightforward to add chemical to this - we have OSCAR and ChemicalTagger which can analyze chunks of running text. And there are  tools for extraction from diagrams. All facts would, of course be Open CC0.

What sort of things would we like to see extracted from the literature? and in what context? possible examples are:
- drugs in a disease context (though diseases are not always well defined
- phytochemistry (this should be both straightforward (se can already extract plant species)
- environment (probably a lookup list)
- chemical syntheses (cf ChemicalTagger http://chemicaltagger.ch.cam.ac.uk)
 
In that context I'd be very interested in simple lists of chemicals that we can use for searching:
- INNs for drugs
- ChEBI entries (Pubchem and Chemspider are too large)
- pesticides and herbicides
- environmental chemicals (VOCs, etc.)

And wherever possible we want to be able to link them back to Wikidata identifiers. So another list is:
- chemicals in Wikipedia

P.


-- 

Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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Egon Willighagen | 7 Mar 13:32 2016
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Twitter account

Hi all,

with all the Open storms around now, which is good, it's important
that the Blue Obelisk stays on the radar. It's doing important things
and if not well-known it will be easily overlooked. And there remains
so much to be done in chemistry...

(BTW, anyone among us going to the upcoming Dutch Open Science
Conference in April? Sadly (for me), I have been put on the waiting
list...)

So, would like to start using the  <at> blueobeliskx account for tweeting
releases of Blue Obelisk software, RT meetings, and the sort. This
account used to be used by the Blue Obelisk eXchange, but because the
Shapado people are missing in action, and my login no longer works,
that (as Rich predicted) is a lost platform at this moment...

Is everyone OK with that? Please let me know if you like access to the
account too, so that others can help with the tweeting and RT-ing.

Egon

--

-- 
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
ORCID: 0000-0001-7542-0286
ImpactStory: https://impactstory.org/EgonWillighagen

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Robert Hanson | 6 Mar 20:34 2016

inchi.js

This is quite cool. Does anyone know how to make it work? What its API looks like? I would like to add this to JSmol. But  when I followed the instructions at

https://github.com/metamolecular/inchi-js

using Firefox I see in the developer console:

Successfully compiled asm.js code (loaded from cache in 148ms)

but no InChI object is present on the page. What am I doing wrong?

Bob Hanson

--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

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Geoffrey Hutchison | 1 Mar 16:56 2016
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Google Summer of Code


OpenChemistry has been accepted into the Google Summer of Code for 2016 - including Open Babel, Avogadro,
cclib and 3DMol.js
https://summerofcode.withgoogle.com/organizations/6290185763422208/
http://wiki.openchemistry.org/GSoC_Ideas_2016

If you are a student and interested in doing open chemistry software development this summer (or know of
someone who is), we're definitely interested in good proposal ideas.

Looking forward to a summer of great science!

Cheers,
-Geoff
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Egon Willighagen | 1 Mar 14:49 2016
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Two Google Summer of Code projects related to the CDK

Hi all,

the NRNB is an USA-based organization around Cytoscape and
WikiPathways, the latter involving PathVisio. You may know that
Cytoscape has a plugin that used the CDK (by Scooter Morris et al.,
UCSF) and here in Maastricht we have been working on PathVisio plugins
for metabolites also using the CDK.

Now, the NRNB has been accepted to the Google Summer of Code and there
are at least two projects where the CDK is related too:

1. https://github.com/nrnb/GoogleSummerOfCode/issues/46
The following project idea is using Java and would involve the CDK directly:

https://github.com/nrnb/GoogleSummerOfCode/issues/46

Here, the idea is integrating a 2D visualization plugin and the
outcome of work by Rianne Fijten for metabolite data (e.g. using the
CDK-based HOSE/NMR prediction stack). These plugins need updating and
integration.

2. https://github.com/nrnb/GoogleSummerOfCode/issues/47
The second idea is in JavaScript where I envision use of remote
services that can convert SMILES and/or identifiers to SVG images of
2D depictions. John's CDKDepict would be a good candidate, but I would
not mind a flexible system that can use other services too, like
perhaps AMBIT.

Now, Noel asked about a JS translation of the CDK stack. That would be
a lot more work, and not sure if it is entirely feasible, but I'm more
than happy to discuss that with the student applicant and co-mentor.

So, if you are a student or know one, please check out these ideas. Of
course, applying does not mean you will get the 5000 dollar to work
for three months during the summer holidays. That's because the NRNB
organization will pick the best proposal (which the students will have
to write). The project ideas are just suggestions, and students are
invited to tune to their interest (though commonly in collaboration
with the anticipated mentor(s)).

Egon

--

-- 
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
ORCID: 0000-0001-7542-0286
ImpactStory: https://impactstory.org/EgonWillighagen

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Andrew Lang | 27 May 23:26 2015
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Blue Obelisk at ACS Boston

Hi Guys:

Is there going to be a Blue Obelisk dinner at ACS Boston? I'll be there Sunday and Monday nights.

Andy Lang

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