chem-bla-ics

Retracted articles cited in Wikipedia

2025-06-08T00:10:00+00:00

Last week, the Wikidata and Sister Projects event tooks place. The presentations are recorded, and I strongly encourage you to check the schedule. One presentation I liked (there are more), was the one by Mike Peel with the title “Best practices for reusing Wikidata’s data in the Wikimedia Projects”. At some point he walks us through the {{Cite Q}} template, around 26:07.

I learned that this template will highlight when an article cited in Wikipedia is actually retracted (withdrawn or replaced). Now, for the past months, I have been using the Crossref API to the Retraction Watch Database and annotated thousands of articles as retracted, using URLs from the database as reference. I use this script.

So, that means that this work actually has had a massive impact. Perhaps thousands of (English) Wikipedia readers have seen the results from running that script. That is pretty awesome! This is why we do open science.

But it made me also wonder something else. The Retraction Watch Database has over 60 thousand articles and Wikidata only about 22 thousand (at the time of writing). What if Wikipedia has an article not in Wikidata? Well, obviously, it cannot use {{Cite Q}}. But wouldn’t we want to have that article in Wikidata? Clearly, the article is notable; at least, in Wikipedia notability-sense. So, I was wondering, of those 40 thousand retracted articles not in Wikidata, how many are cited in English Wikipedia (to start with).

So, I wrote a first script that lists DOIs in the Retraction Watch Database (via the CrossRef API downloaded list) that are not found in Wikidata. A second script uses a Scholia (doi:10.1007/978-3-319-70407-4_36) SPARQL query develop by Finn Nielsen that uses wikibase:mwapi to do an efficient DOI search.

The results are fascinating and this is the list of DOIs found:

Searching 10.1016/j.engfailanal.2021.105457 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Filippo_Berto
Searching 10.1002/14651858.CD002291 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Antipruritic
Searching 10.1007/s12115-020-00496-1 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Lawrence_Mead
Searching 10.1515/9783110619768 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Dead_Eagle_Owl
Searching 10.1016/j.sbi.2022.102426 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Deborah_F._Kelly
Searching 10.1371/journal.pone.0240851 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Industrialization_of_China
Searching 10.1080/00927670309601525 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Rouben_Azizian
Searching 10.1080/14693062.2016.1179616 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Benjamin_K._Sovacool
Searching 10.1038/s41390-022-02127-3 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Harald_Walach
Searching 10.1001/jamapediatrics.2021.2659 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Harald_Walach
Searching 10.1109/CCECE.2007.335 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/List_of_scientific_misconduct_incidents
Searching 10.1002/14651858.CD001834 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Meningococcal_vaccine
Searching 10.1007/s11356-021-16530-6 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Kamran_Bagheri_Lankarani
Searching 10.1016/j.biortech.2023.129044 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Ashok_Pandey
Searching 10.1002/14651858.CD003614 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Trimetazidine
Searching 10.1002/14651858.CD003808 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Hall_Technique
Searching 10.1002/14651858.CD003747 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Venous_thrombosis
Searching 10.1002/14651858.CD003711 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Myocarditis
Searching 10.1002/14651858.CD003225 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Prevention_of_migraine_attacks
Searching 10.1002/14651858.CD003226 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Prevention_of_migraine_attacks
Searching 10.1002/14651858.CD003498 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/A2_milk
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Autism
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Autism_therapies
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Casein
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Casomorphin
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Causes_of_autism
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Gluten-free%2C_casein-free_diet
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Gluten-free_diet
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Opioid_excess_theory
Searching 10.1093/restud/rdy054 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Managerial_economics
Searching 10.1039/d1nr00388g in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Deborah_F._Kelly
Searching 10.1139/p90-116 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Canada%27s_Stonehenge
Searching 10.3791/64256 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Thomas_J._Webster
Searching 10.1016/j.biortech.2022.127565 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Ashok_Pandey
Searching 10.1016/j.anbehav.2015.04.001 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Stegodyphus_dumicola
Searching 10.1016/j.tafmec.2022.103573 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Filippo_Berto
Searching 10.1155/2022/7002630 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Dopamine_receptor_D3
Searching 10.1007/s11223-017-9884-2 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Filippo_Berto
Searching 10.1016/j.forsciint.2024.112115 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Peter_A._McCullough
Searching 10.1002/14651858.CD002778 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Temporomandibular_joint_dysfunction
Searching 10.1016/j.jcv.2022.105248 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Kay_Davies
Searching 10.1002/14651858.CD002916 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Bleomycin
Searching 10.1007/s11756-021-00841-7 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/2021_in_archosaur_paleontology
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Argentinadraco
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Wellnhopterus
Searching 10.4132/KoreanJPathol.2009.43.4.306 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Cho_Kuk
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Cho_Min_academic_credentials_scandal
Searching 10.1503/cmaj.80742 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/LetUsTalk
Searching 10.1002/14651858.CD004125 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Granisetron
Searching 10.1111/ffe.12616 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Filippo_Berto
Searching 10.1007/s00366-008-0118-x in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Kamran_Daneshjoo
Searching 10.1002/jmv.28097 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Noora_%28vaccine%29
Searching 10.1126/science.1070563 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Sch%C3%B6n_scandal
Searching 10.1246/cl.170853 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Enantioselective_Iridium-Catalyzed_C-H_Borylation
Searching 10.1016/j.marpol.2017.06.032 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Ray_Hilborn
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Tony_J._Pitcher
Searching 10.1016/j.ijfatigue.2021.106450 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Filippo_Berto
Searching 10.1016/j.crphar.2022 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Desidustat
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Emoxypine
Searching 10.1007/s10479-023-05261-1 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Artificial_intelligence_marketing
Searching 10.1257/aer.20210369 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Dividend_tax
Searching 10.1109/AIMSEC.2011.6010222 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/SAP_CRM
Searching 10.1002/14651858.CD001103 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Hydrocolloid_dressing
Searching 10.1007/978-3-642-27708-5 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/IP_Multimedia_Subsystem
Searching 10.1351/PAC-CON-08-12-06 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Parthenocissus_tricuspidata
Searching 10.1002/advs.202204315 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Tetrataenite
Searching 10.1353/sho.2011.0038 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Maus
Searching 10.1111/jpim.12058 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Ulrich_Lichtenthaler
Searching 10.1136/bcr-2021-241572 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/COVID-19_proxalutamide_trial_in_Brazil
Searching 10.1038/s44160-022-00068-7 in Wikipedia...
  ... found in this Wikipedia page: https://en.wikipedia.org/wiki/Single-layer_materials

Chemistry Central and the ORCID identifier

2015-04-18T00:00:00+00:00

If you are a scientist you have heard about the ORCID identifier by now. If not, you have been focusing on groundbreaking research and isolated yourself from the rest of the world, just to make it perfect and get that Nobel prize next year. If you have been working on impactful research, Nobel prize-worthy, and have been blogging and tweeting about your progress, as a good Open Scholar, you know ORCID is the DOI for “research contributors” and you already have one yourself, and probably also that T-shirt with your own identifier. Mine is 0000-0001-7542-0286, and almost 1.3M other authors got one too. The list of ORCIDs on Wikipedia is growing (and Wikidata), thanks to Andy Mabbett, whom also made it possible to add your ORCID on WikiPathways.

Anyway, what I was pleased to see today that you can now log in with your ORCID identifier with the Chemistry Central article submission system (notice the green icon):

Many other publishers allow logging in with your ORCID too, which benefits many:

authors who just enter a list of ORCID identifiers, instead of a long list of author names and affiliations
publishers, which have a simpler submission system and get more accurate information about submitters
funding agencies which can more easily track what is done with the research funding
research institutes which can more easily track what their employees are studying

Don’t have one yet? Get your very own ORCID here.

“Royal Society of Chemistry grants journals access to Wikipedia Editors”

2015-01-09T00:00:00+00:00

The Royal Society of Chemistry and Wikipedia just released an interesting press release:

“The Royal Society of Chemistry has announced that it is donating 100 “RSC Gold” accounts – the complete portfolio of their journals and databases – to be used by Wikipedia editors who write about chemistry. The partnership is part of a wider collaboration between the Society’s members and staff, Wikimedia UK and the Wikimedia community. The collaboration is working to improve the coverage of chemistry-related topics on Wikipedia and its sister projects.”

This leaves me with a lot of questions. I asked these in a comment awaiting moderation:

Can you elaborate on the conditions? Is it limited to wikipedia.org or does it extend to other Wikimedia projects, like Wikidata? Does the agreement allow manual lookup of information only, or does it allow text mining on the literature as well as on the database? How should I put this in perspective with the UK law that allows text mining, and, in particular, can UK Wikipedia editors use text mining anyway, or is that restricted? Is there an overview of the details of what is allowed and not allowed, or a list of restrictions otherwise?

Details on how to apply to access can be found here.

Downloading Domoic Acid from PubChem

2009-04-17T00:10:00+00:00

The identity of domoic acid has been under discussion (see here, here and here). (And I very much like the ChemSpider service to make it easy to copy data from ChemSpider into WikiPedia ChemBoxes; cheers!)

Now, my practical in next weeks CDK Workshop will use Groovy (please install it on your laptop!), and am hacking up example scripts for the course material, and came up with this script to download the structure of domoic acid from PubChem (CID:5282253):

DBPedia: lookup and autocomplete of chemistry

2009-02-11T00:00:00+00:00

On the DBPedia discussion mailing list there was a post on a nice web page which allows you to look up things, and which features a autocomplete edit field. The below screenshot show lookup of molecular structures:

If you are not ware of this, adding content to DBPedia is as easy as adding something to WikiPedia. Literally: DBPedia is the RDF flavour of WikiPedia. It extracts the information from the info boxes, as I discussed before (see Molecules in Wikipedia).

BTW, one can take advantage of DBPedia to see what WikiPedia has to offer in terms of chemistry. For example, to list all molecules which have a SMILES, one can use this simple SPARQL query:

Or, to list those which have an InChI:

And this is actually quite useful, e.g. it can be used in quality control. Running the above queries will show up several broken SMILES and InChIs. I have not had time to fix those yet, so please go ahead and beat me to those fixes, and get some WikiPedia Fame :) Alternatively, invert the queries and add missing InChIs, PubChem CID or SMILES. When I have a bit more free time again, after the new stable CDK and Bioclipse releases, I’ll runs these analyses again, and summarize them in a web page.

Molecules in Wikipedia without InChIs #3

2007-11-16T00:00:00+00:00

Third in the series of blogs about molecules in Wikipedia without an InChI (see also #1 and #2 ). There a certainly false positives, but here’s the updated list:

http://www.en.wikipedia.org/wiki/AZD2171
http://www.en.wikipedia.org/wiki/Alizarin
http://www.en.wikipedia.org/wiki/Allantoin
http://www.en.wikipedia.org/wiki/Allylamine
http://www.en.wikipedia.org/wiki/Alpha-ethyltryptamine
http://www.en.wikipedia.org/wiki/Anthraquinone
http://www.en.wikipedia.org/wiki/Aspartame
http://www.en.wikipedia.org/wiki/Barium_sulfate
http://www.en.wikipedia.org/wiki/Biotin
http://www.en.wikipedia.org/wiki/Boron_nitride
http://www.en.wikipedia.org/wiki/Botox
http://www.en.wikipedia.org/wiki/Bremelanotide
http://www.en.wikipedia.org/wiki/CAS_registry_number
http://www.en.wikipedia.org/wiki/Cadmium_sulfide
http://www.en.wikipedia.org/wiki/Carminic_acid
http://www.en.wikipedia.org/wiki/Celestine_%28mineral%29
http://www.en.wikipedia.org/wiki/Cellulose
http://www.en.wikipedia.org/wiki/Chemical
http://www.en.wikipedia.org/wiki/Chemical_file_format
http://www.en.wikipedia.org/wiki/Cheminformatics
http://www.en.wikipedia.org/wiki/Chloramine
http://www.en.wikipedia.org/wiki/Chloroethane
http://www.en.wikipedia.org/wiki/Cinnamic_acid
http://www.en.wikipedia.org/wiki/Crabtree's_catalyst
http://www.en.wikipedia.org/wiki/DDT
http://www.en.wikipedia.org/wiki/DMAP
http://www.en.wikipedia.org/wiki/Dimethicone#Applications
http://www.en.wikipedia.org/wiki/Dimethyl_amine
http://www.en.wikipedia.org/wiki/Dimethyl_sulfide
http://www.en.wikipedia.org/wiki/Dimethylethanolamine
http://www.en.wikipedia.org/wiki/Dioxine
http://www.en.wikipedia.org/wiki/Diphenylamine
http://www.en.wikipedia.org/wiki/Dmso
http://www.en.wikipedia.org/wiki/EDTA
http://www.en.wikipedia.org/wiki/Eschenmoser%27s_salt
http://www.en.wikipedia.org/wiki/Ethylene_carbonate
http://www.en.wikipedia.org/wiki/Folate
http://www.en.wikipedia.org/wiki/Formic_acid
http://www.en.wikipedia.org/wiki/HMPA
http://www.en.wikipedia.org/wiki/Hafnium(IV)_oxide
http://www.en.wikipedia.org/wiki/Heavy_water
http://www.en.wikipedia.org/wiki/Hexafluoroisopropanol
http://www.en.wikipedia.org/wiki/Hydrogen_cyanide
http://www.en.wikipedia.org/wiki/Hydrogen_cyanide#Hydrogen_cyanide_as_a_chemical_weapon
http://www.en.wikipedia.org/wiki/Hydrogen_peroxide
http://www.en.wikipedia.org/wiki/Hydroxyapatite
http://www.en.wikipedia.org/wiki/Hydroxybenzotriazole
http://www.en.wikipedia.org/wiki/IUPAC_nomenclature_of_inorganic_chemistry
http://www.en.wikipedia.org/wiki/Indole
http://www.en.wikipedia.org/wiki/Interferon_beta-1a
http://www.en.wikipedia.org/wiki/J%C3%B6ns_Jakob_Berzelius
http://www.en.wikipedia.org/wiki/Lawesson%27s_reagent
http://www.en.wikipedia.org/wiki/Lewisite
http://www.en.wikipedia.org/wiki/MTBE
http://www.en.wikipedia.org/wiki/Maitotoxin
http://www.en.wikipedia.org/wiki/Menthol
http://www.en.wikipedia.org/wiki/Merck_Index
http://www.en.wikipedia.org/wiki/Mescaline
http://www.en.wikipedia.org/wiki/Metaldehyde
http://www.en.wikipedia.org/wiki/Methionylalanylthreonyl...leucine
http://www.en.wikipedia.org/wiki/Methyl_amine
http://www.en.wikipedia.org/wiki/Methyl_salicylate
http://www.en.wikipedia.org/wiki/Molecular_Query_Language
http://www.en.wikipedia.org/wiki/N-butyllithium
http://www.en.wikipedia.org/wiki/Nafion
http://www.en.wikipedia.org/wiki/Nitrous_oxide
http://www.en.wikipedia.org/wiki/Octanitrocubane
http://www.en.wikipedia.org/wiki/Organic_chemistry
http://www.en.wikipedia.org/wiki/Organic_chemistry#Molecular_structure_elucidation
http://www.en.wikipedia.org/wiki/P4O10
http://www.en.wikipedia.org/wiki/Paraldehyde
http://www.en.wikipedia.org/wiki/Penicillin
http://www.en.wikipedia.org/wiki/Peroxyacetic_acid
http://www.en.wikipedia.org/wiki/Phenol
http://www.en.wikipedia.org/wiki/Physical_science
http://www.en.wikipedia.org/wiki/Piperidine
http://www.en.wikipedia.org/wiki/Potassium_chloride
http://www.en.wikipedia.org/wiki/Psilocybin
http://www.en.wikipedia.org/wiki/Pubchem
http://www.en.wikipedia.org/wiki/Quinine_total_synthesis
http://www.en.wikipedia.org/wiki/Resveratrol
http://www.en.wikipedia.org/wiki/Rhodamine
http://www.en.wikipedia.org/wiki/Salvia_divinorum
http://www.en.wikipedia.org/wiki/Selenium_dioxide
http://www.en.wikipedia.org/wiki/Silicon_carbide
http://www.en.wikipedia.org/wiki/Skatole
http://www.en.wikipedia.org/wiki/Skeletal_formula
http://www.en.wikipedia.org/wiki/Soman
http://www.en.wikipedia.org/wiki/Splenda
http://www.en.wikipedia.org/wiki/Standard_atomic_weight
http://www.en.wikipedia.org/wiki/Subgraph_isomorphism_problem
http://www.en.wikipedia.org/wiki/Sulfur_hexafluoride
http://www.en.wikipedia.org/wiki/Sulfur_mustard
http://www.en.wikipedia.org/wiki/TBHQ
http://www.en.wikipedia.org/wiki/Tabun_(nerve_agent)
http://www.en.wikipedia.org/wiki/Teicoplanin
http://www.en.wikipedia.org/wiki/Tetra-ethyl_lead
http://www.en.wikipedia.org/wiki/Tetraazidomethane
http://www.en.wikipedia.org/wiki/Tetrachloroethylene
http://www.en.wikipedia.org/wiki/Thiomersal
http://www.en.wikipedia.org/wiki/Titanium_dioxide
http://www.en.wikipedia.org/wiki/Tourmaline
http://www.en.wikipedia.org/wiki/Uric_acid
http://www.en.wikipedia.org/wiki/VX_%28nerve_agent%29
http://www.en.wikipedia.org/wiki/Valence_%28chemistry%29
http://www.en.wikipedia.org/wiki/benzylbromide
http://www.en.wikipedia.org/wiki/cortisone
http://www.en.wikipedia.org/wiki/epothilone
http://www.en.wikipedia.org/wiki/piperidine
http://www.en.wikipedia.org/wiki/stilbene
http://www.wikipedia.org/wiki/Phosgene

Molecules in Wikipedia without InChIs

2007-08-11T00:00:00+00:00

I reported last week about the Molecules in Wikipedia and the plethora of templates used. Chemical blogspace has also been using Wikipedia URLs as molecular identifier and extracting InChIs from the wiki pages (see Using Wikipedia to recognize Molecules in Blogspace ). Several people have shown interest in adding InChIs for molecules in Wikipedia, so here’s a new version of a list it molecules without InChIs:

http://www.en.wikipedia.org/wiki/Hydrogen_cyanide#Hydrogen_cyanide_as_a_chemical_weapon -> but no InChI/CID
http://www.en.wikipedia.org/wiki/P-Phenylenediamine -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Valence_%28chemistry%29 -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Nitrous_oxide -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Cytisine -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Disulfur_decafluoride -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Mescaline -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Lewisite -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Sulfur_mustard -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Tryptamine -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Interferon_beta-1a -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Methyl_isocyanate -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Anthraquinone -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Tocopherol -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Cinnamic_acid -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Tryptamine -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Psilocybin -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Alphamethyltryptamine -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Alpha-ethyltryptamine -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Allylamine -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Ergosterol -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Squalene -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Sulfur_hexafluoride -> but no InChI/CID

Strictly speaking, the list should be longer, as the code that produced this list actually is also happy when a PubChem compound identifier (CID) is given. The previous list is also still online .

Molecules in Wikipedia

2007-08-02T00:00:00+00:00

I do not care about physical and chemical properties in Wikipedia, as I can easily extract them from other sources. The main value of Wikipedia for molecules is, I think, that it describes the history of a molecule. Additionally, the Wikipedia URL is a nice unique molecular identifier (for example http://en.wikipedia.org/wiki/Lactose) given certain conditions, and many bloggers are using it as such . But, it only is a useful identifier if one (and only one) InChI is stated on the wiki page.

Now that I am RDF-ing molecular space , I was again interested in dbpedia, a RDF version of Wikipedia. See these two blog items and Peter’s very nice dbpedia, RDF and SPARQL - for chemistry item. Christian is picking this up, and extending dbpedia for support for the various chemical boxes.

Wikipedia Templates

I have spotted a couple of templates: Drugbox, Chembox, Chembox new, of which the last one seems to most recent, and has extensions for explosives and drugs. The WikiProject Chemicals does not mention it though. Anyone who knows the status? Is chembox new the way forward and going to replace the older chembox? I hope so, because only the newer one has InChI in the last of official fields. Or is chembox new simply an extension of chembox itself?

Somewhere between 1000 and 1500 entries use the chembox new and another 1000 to 1500 use chembox but I assume there is considerable overlap. Additionally, Christian noted that there still seem to be molecules in Wikipedia which do not use a template at all, and counted some 1900 molecules using various lists. If you you want to keep a more close eye on chemistry in dbpedia, you should register to the dbpedia-discussion mailing list.

Using Wikipedia to recognize Molecules in Blogspace

2007-06-19T00:00:00+00:00

Only few people are using InChI’s to indicate the molecules the blog about (prominent exceptions are Useful Chemistry and Molecule of the Day). Consequently, the number of detected molecules (without using OSCAR3) in Chemical blogspace has been low.

Fortunately, many more people use links to Wikipedia to identify the molecules that talk about. And some of these pages use the ChemBox template which actually might contain a PubChem CID or even an InChI. This has increased the molecular content of Chemical blogspace considerably.

There is also, however, a good list of molecules in Wikipedia for which no CID or InChI is given:

http://www.en.wikipedia.org/wiki/Hafnium(IV)_oxide -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Cubane -> but no InChI/CID
http://www.en.wikipedia.org/wiki/water -> but no InChI/CID
http://www.en.wikipedia.org/wiki/oxidane -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Carminic_acid -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Alizarin -> but no InChI/CID
http://www.en.wikipedia.org/wiki/AIBN -> but no InChI/CID
http://www.en.wikipedia.org/wiki/piperidine -> but no InChI/CID
http://www.en.wikipedia.org/wiki/hydroxide -> but no InChI/CID
http://www.en.wikipedia.org/wiki/tetrahydrocannabinol -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Epibatidine -> but no InChI/CID
http://www.en.wikipedia.org/wiki/cortisone -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Eschenmoser%27s_salt -> but no InChI/CID
http://www.en.wikipedia.org/wiki/pyrrole -> but no InChI/CID
http://www.en.wikipedia.org/wiki/anthracene -> but no InChI/CID
http://www.en.wikipedia.org/wiki/benzylbromide -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Skatole -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Teicoplanin -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Methyl_violet -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Penicillin -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Aspartame -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Splenda -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Sucrose -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Rhodamine -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Ascorbic_acid -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Tabun_(nerve_agent) -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Soman -> but no InChI/CID
http://www.wikipedia.org/wiki/Phosgene -> but no InChI/CID
http://www.en.wikipedia.org/wiki/AZD2171 -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Heavy_water -> but no InChI/CID
http://www.en.wikipedia.org/wiki/MTBE -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Biotin -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Spermine -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Silicon_carbide -> but no InChI/CID
http://www.en.wikipedia.org/wiki/stilbene -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Methyl_salicylate -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Dmso -> but no InChI/CID
http://www.en.wikipedia.org/wiki/DMF -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Acetonitrile -> but no InChI/CID
http://www.en.wikipedia.org/wiki/HMPA -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Phenol -> but no InChI/CID
http://www.en.wikipedia.org/wiki/TBHQ -> but no InChI/CID
http://www.en.wikipedia.org/wiki/MTBE -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Salvia_divinorum -> but no InChI/CID
http://www.en.wikipedia.org/wiki/salvinorin -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Tetrahydrocannabinol -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Selenium_dioxide -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Piperidine -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Resveratrol -> but no InChI/CID
http://www.en.wikipedia.org/wiki/P4O10 -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Dimethyl_sulfide -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Folate -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Hydroxybenzotriazole -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Hydrogen_cyanide -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Peroxyacetic_acid -> but no InChI/CID
http://www.en.wikipedia.org/wiki/epothilone -> but no InChI/CID
http://www.en.wikipedia.org/wiki/paraquat -> but no InChI/CID
http://www.en.wikipedia.org/wiki/N-butyllithium -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Nafion -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Boron_nitride -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Triclosan -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Hydrogen_peroxide -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Cholesterol -> but no InChI/CID
http://www.en.wikipedia.org/wiki/DMAP -> but no InChI/CID
http://www.en.wikipedia.org/wiki/aniline -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Phenol -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Ascorbic_acid -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Nicotine -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Tetra-ethyl_lead -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Acetophenone -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Ethanol -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Acetaldehyde -> but no InChI/CID
http://www.en.wikipedia.org/wiki/EDTA -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Menthol -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Formic_acid -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Octanitrocubane -> but no InChI/CID
http://www.en.wikipedia.org/wiki/VX_%28nerve_agent%29 -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Tetraazidomethane -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Lawesson%27s_reagent -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Hexafluoroisopropanol -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Cellulose -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Bremelanotide -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Cellulose -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Dimethicone#Applications -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Shikimic_acid -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Methyl_amine -> but no InChI/CID
http://www.en.wikipedia.org/wiki/Dimethyl_amine -> but no InChI/CID
http://www.en.wikipedia.org/wiki/DDT -> but no InChI/CID

I really would like to start adding InChI’s for these molecules to Wikipedia, but someone needs to enlighten me about the state of ChemBox? Can the InChI be added to the template, or should the InChI be given elsewhere on the page? Adding such small bits is easier than writing a full entry.