Comments on: Hacking PubChem – Technology Easy, Quality Difficult http://www.chemspider.com/blog/hacking-pubchem-technology-easy-quality-difficult.html Building Community for Chemists Fri, 10 Feb 2012 11:07:05 +0000 hourly 1 http://wordpress.org/?v=3.1.2 By: ChemSpider Blog » Blog Archive » STOP COUNTING the Number of Chemical Entities in Public Compound Databases and There are Ghosts in the Closet http://www.chemspider.com/blog/hacking-pubchem-technology-easy-quality-difficult.html/comment-page-1#comment-188314 ChemSpider Blog » Blog Archive » STOP COUNTING the Number of Chemical Entities in Public Compound Databases and There are Ghosts in the Closet Sat, 11 Jul 2009 19:46:42 +0000 http://www.chemspider.com/blog/?p=137#comment-188314 [...] simple example is that of methane in PubChem that I have blogged about many times…one example here. Here are some of the names associated with the structure of methane on PubChem: [...] [...] simple example is that of methane in PubChem that I have blogged about many times…one example here. Here are some of the names associated with the structure of methane on PubChem: [...]

]]> By: A naive biochemist wakes up to the closed world of chemical abstracts and such « The Omics world http://www.chemspider.com/blog/hacking-pubchem-technology-easy-quality-difficult.html/comment-page-1#comment-125819 A naive biochemist wakes up to the closed world of chemical abstracts and such « The Omics world Fri, 05 Dec 2008 16:19:08 +0000 http://www.chemspider.com/blog/?p=137#comment-125819 [...] providers using a suitable lookup id . Naively I assumed this would be the CAS id which is the “unique id” associated with each molecule . An hour of googling later I woke up to the realization that CAS is [...] [...] providers using a suitable lookup id . Naively I assumed this would be the CAS id which is the “unique id” associated with each molecule . An hour of googling later I woke up to the realization that CAS is [...]

]]> By: ChemSpider Blog » Blog Archive » Enforcing Copyright of CAS Numbers http://www.chemspider.com/blog/hacking-pubchem-technology-easy-quality-difficult.html/comment-page-1#comment-24350 ChemSpider Blog » Blog Archive » Enforcing Copyright of CAS Numbers Sun, 09 Mar 2008 07:07:21 +0000 http://www.chemspider.com/blog/?p=137#comment-24350 [...] ID” for a compound. Check out my earlier posts about the need for curation (1,2,3,4 and many others). CAS is very highly curated and are the authority for the CAS numbers. PubChem [...] [...] ID” for a compound. Check out my earlier posts about the need for curation (1,2,3,4 and many others). CAS is very highly curated and are the authority for the CAS numbers. PubChem [...]

]]> By: Unilever Centre for Molecular Informatics, Cambridge - petermr’s blog » Blog Archive » Comments on comments and agents and eyeballs http://www.chemspider.com/blog/hacking-pubchem-technology-easy-quality-difficult.html/comment-page-1#comment-3010 Unilever Centre for Molecular Informatics, Cambridge - petermr’s blog » Blog Archive » Comments on comments and agents and eyeballs Mon, 01 Oct 2007 19:10:48 +0000 http://www.chemspider.com/blog/?p=137#comment-3010 [...] ChemSpiderMan Says: October 1st, 2007 at 3:55 pm ePeter, I’ve given many examples of the issue of Data Quality on the blog. Some links are:http://www.chemspider.com/blog/?p=64 http://www.chemspider.com/blog/?p=164 http://www.chemspider.com/blog/?p=168 http://www.chemspider.com/blog/?p=137 [...] [...] ChemSpiderMan Says: October 1st, 2007 at 3:55 pm ePeter, I’ve given many examples of the issue of Data Quality on the blog. Some links are:http://www.chemspider.com/blog/?p=64 http://www.chemspider.com/blog/?p=164 http://www.chemspider.com/blog/?p=168 http://www.chemspider.com/blog/?p=137 [...]

]]> By: Egon Willighagen http://www.chemspider.com/blog/hacking-pubchem-technology-easy-quality-difficult.html/comment-page-1#comment-2542 Egon Willighagen Sun, 16 Sep 2007 06:27:24 +0000 http://www.chemspider.com/blog/?p=137#comment-2542 Yet another reason to use InChI instead. I *know* a lot of people use the CAS registry number as identifiers; some people also can't stop smoking/drinking/... To use Rich blog of last week: InChI is to chemoinformatics what the pass forward was to football. And this blog item shows the score :) Cheers! Yet another reason to use InChI instead. I *know* a lot of people use the CAS registry number as identifiers; some people also can’t stop smoking/drinking/…

To use Rich blog of last week: InChI is to chemoinformatics what the pass forward was to football. And this blog item shows the score :)

Cheers!

]]> By: Antony Williams http://www.chemspider.com/blog/hacking-pubchem-technology-easy-quality-difficult.html/comment-page-1#comment-2491 Antony Williams Fri, 14 Sep 2007 22:41:06 +0000 http://www.chemspider.com/blog/?p=137#comment-2491 A friend sent me these comments offline "Some of those seem to be formulations for CH4 and a non-structured component. This is one of the most common ways that CAS numbers get associated improperly. I seem to recall that Methane is simply 74-82-8, not even in your subset." He is right that 74-82-8 is not in the subset but it is bolded and is the FIRST of all of the synonyms showing that it has been validated by a curator A friend sent me these comments offline “Some of those seem to be formulations for CH4 and a non-structured component. This is one of the most common ways that CAS numbers get associated improperly. I seem to recall that Methane is simply 74-82-8, not even in your subset.”

He is right that 74-82-8 is not in the subset but it is bolded and is the FIRST of all of the synonyms showing that it has been validated by a curator

]]> By: Joerg Kurt Wegner http://www.chemspider.com/blog/hacking-pubchem-technology-easy-quality-difficult.html/comment-page-1#comment-2480 Joerg Kurt Wegner Fri, 14 Sep 2007 17:16:00 +0000 http://www.chemspider.com/blog/?p=137#comment-2480 Agreed! This gives a *big* minus for PubChem. Are they really expecting that others find the duplicates and the wrong structures? Anyway, can you not offer something for this? E.g. another web-service called "Check pubchem cid in curated chemspider data" And thanks for *doing* this http://www.chemspider.com/blog/?p=135 You could even go a step further by offering a service called "return curated unique inchikey or chemspider csid from non-curated pubchem cid"! Agreed! This gives a *big* minus for PubChem. Are they really expecting that others find the duplicates and the wrong structures?

Anyway, can you not offer something for this? E.g. another web-service called “Check pubchem cid in curated chemspider data”

And thanks for *doing* this
http://www.chemspider.com/blog/?p=135

You could even go a step further by offering a service called “return curated unique inchikey or chemspider csid from non-curated pubchem cid”!

]]> By: Rich Apodaca http://www.chemspider.com/blog/hacking-pubchem-technology-easy-quality-difficult.html/comment-page-1#comment-2473 Rich Apodaca Fri, 14 Sep 2007 15:38:46 +0000 http://www.chemspider.com/blog/?p=137#comment-2473 The question of quality will always be present in any database, and your post raises valid concerns. It _would_ be great if CAS created a free Web service for CAS number lookup. In fact, such a move might just save their franchise. I've seen many examples of the same substance having multiple CAS numbers - it's quite common. It might be interesting for a reader with access to SciFinder to get a list of all of the CAS numbers for methane. Clearly, many of those CAS numbers are for "Carbon" and its mixtures/derivatives/allotropes - which could be attributed to the molfile format not having a consistent way to represent implicit hydrogens. (The data format used for compound registration matters - a lot). So the methane example may be the worst case scenario for a molecule unlikely to appear in most databases. During the transition away from CAS numbers as a chemical identifier, conversions such as CAS number-> PubChem CID (or CAS number-> IUPAC name) will become very important. PubChem records contain IUPAC names (in several flavors), so it might be possible to use that field as a consistency check - as you've done. Bottom line: limbo-land is where we're at. As the Chinese say, may you live in interesting times... The question of quality will always be present in any database, and your post raises valid concerns. It _would_ be great if CAS created a free Web service for CAS number lookup. In fact, such a move might just save their franchise.

I’ve seen many examples of the same substance having multiple CAS numbers – it’s quite common. It might be interesting for a reader with access to SciFinder to get a list of all of the CAS numbers for methane. Clearly, many of those CAS numbers are for “Carbon” and its mixtures/derivatives/allotropes – which could be attributed to the molfile format not having a consistent way to represent implicit hydrogens. (The data format used for compound registration matters – a lot). So the methane example may be the worst case scenario for a molecule unlikely to appear in most databases.

During the transition away from CAS numbers as a chemical identifier, conversions such as CAS number-> PubChem CID (or CAS number-> IUPAC name) will become very important. PubChem records contain IUPAC names (in several flavors), so it might be possible to use that field as a consistency check – as you’ve done.

Bottom line: limbo-land is where we’re at. As the Chinese say, may you live in interesting times…

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