here has been a response to my post about Chemical Names and Structures here.
PMR>”For certain purposes, it is valuable to collect as many names as possible, for example for location of lookup. But these should be accompanied with metadata. A similar example is from ChemSpiderMan (ed.):
On a record view we list “Names and Synonyms”. The question marks Peter sees are for a French name shown here: Looks fine in my broswer and pasted in here too: N-{2-[({5?-[(dim�th?ylamino)m?�thyl]fur?an-2-yl}m?�thyl)sul?fanyl]�th?yl}-N’-m�?thyl-2-ni?tro�th�ne?-1,1-diam?ine. So, not junk (saying that the French name is junk would offend the Parisians). Notice that the Z- has been removed (for now) and that the name is labeled French on the record. If any of you are seeing issues in your browser let us know and we will investigate at our end.
PMR: Without the metadata giving the langauage information is losr. For example what does “pain” mean? If the language is not given there is a tendency to interpret this as english. We have to acknowledge that the language of science is currently english (it wasn’t when I started and we had to read French and German papers). So RDF, for example, provides a language qualifier (e.g. @en or @fr). The addition of that qualifier transforms the information from junk to meaningful. “
First of all, it’s interesting to note that the French name has been rendered as “junk” in Peter’s blog as shown here.
This probably relates to his original comment that the name is junk in his browser too…but acceptable in mine. On the other hand his blog post may look fine to him and looks bad in mine! Oh those dependencies…I see similar things show up in WordPress regularly.
Peter suggests that there should be metadata giving the language information. Good idea. See my previous blog post about that particular issue and the fact that we allow curators to layer on metadata AND we capture and retain it WHEN it is available.
If you look at this record you will see that there are names labeled as Polish, German and Dutch.
Chloroprene [Wiki]
1,3-Butadiene, 2-chloro-
126-99-8 [RN]
204-818-0 [EINECS]
2-Chloor-1,3-butadieen [Dutch]
2-Chlor-1,3-butadien [German]
2-Chlorbuta-1,3-dien [German]
2-Chloro-1,3-butadiene
2-Chlorobutadiene
Chloropren [Polish]
Most labels were captured during the deposition process. One was added manually.Notice also the direct links to Wikipedia, the Registry number link to perform a search of PubChem and the link to EINECS.
As I commented in my post on ranitidine, and extracting from Peter’s post “Notice …….. that the name is labeled French on the record.” So, what Peter suggests is already in place on ChemSpider. I display below what is presently available to curators to label the names with. Notice this includes language,
EINECS numbers, CAS Registry Numbers, INNs, JANs etc.
The list of languages is easy to expand. Anybody have any requests?
A further comment “PMR: I very much like the idea of regarding chemical names as social identifiers. But, of course, that only works for humans. The machines can aggregate the tags but they cannot make inferences from them. The problem is that when they are put into databases they lose their social context and are managed by hard boolean logic. That fails immediately and often dramatically. A major cause is the loss of metadata and authorities. In this world you cannot use voting (which is why Chempedia cannot be seen as an authority for CAS numbers, only a useful guide). We have to use authorities (provenance) in our information. Thus the statements: Ranitidine is the Z-isomer and Ranitidine is the E-isomer may be seen as contradictory. That’s why people have suggested that RDF should have quads, not triples, such as Antony_Williams asserts ranitidine hasIsomer Z Wikipedia asserts ranitidine hasIsomer E Both these are true. That is the language we should use in the semantic web PeterMR still deliberately fails to make an assertion about this isomerism and is waiting to see what others think.”
This leads us into a deeper discussion about retention of metadata and authorities. We retain metadata when it is deposited or we can harvest it. Let’s consider the information below extracted from the same compound on ChemSpider:
Notice all of the 
and note that they all link through to the original source of information, in this case NIOSH.
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Visual appearance of the given substance.
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There are also properties and each piece of data links out to the original source.For this record it is the same source. For some records it is already multiple sources.
Experimental physchem properties
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The boiling point of a liquid is the temperature at which the vapor pressure of the liquid equals the environmental pressure surrounding the liquid. See also: Boiling Point
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The flash point of a flammable liquid is the lowest temperature at which it can form an ignitable mixture in air. See also: Flash Point
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Specific gravity is defined as the ratio of the density of a given substance to the density of water, when both are at the same temperature. See also: Specific Gravity
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This particular structure has been deposited onto the ChemSpider database a total of 18 times from the source databases listed below. Where possible i.e. when the structure is available online on the suppliers website and can be hyperlinked to, then each external ID links to the depositor. There is an error! The Aldrich depositions are for the polymer forms! Curators can know this info out.
Also available to master curators is the ability to see who has been editing the names and synonyms and a full record of depositions, by who and when.
So, names are labeled with language and links to Wikipedia and other info. The predicted properties and systematic name are generally labeled according to the provider of the algorithm(s). We keep track of every URL and publication deposition and know which user deposited what and when…if the site is “vandalized” then we know which user did so.
Overall I’d say we have a lot of metadata for this record. The same is true for tens of thousands of records on ChemSpider and the amount of such information is growing literally daily. We’re not done yet of course – there is much more to add. We put a lot of thought into the design of this system and associated metadata but we also chose to jump off the cliff and start “doing”. There is a lot to learn from managing 20 million molecules and the complexity that comes with doing so. We continue to morph and extend as necessary and welcome input.
To clarify re. ranitidine…. I am NOT asserting that ranitidine has Z-isomer. I am stating that ranitidine has multiple names on ChemSpider, some with no stereochemistry and some with Z-stereochemistry. I also
report that a published crystal structure reports a Z-orientation. I also report that a commercial software package suggests that the three tautomeric structures below are possible for ranitidine.
I also report, just for fun of course, that the InChI algorithm will declare two of these isomers, the bottom two, as equivalent when “mobile protons” are taken into account. Compare the ON InChIKeys below when mobile proton perception is detected by the InChI algorithm. Need more information?
With the curation capabilities we have in place, with the retained metadata, linkages to depositors and other sites and the revision history available, I would say that we are well equipped to manage the data for chemists and continue to enhance our platform for chemists worldwide.
Many of us using ChemSpider are looking for compounds of interest to us. In some cases those chemical entities are not of fleeting interest but something that we are working on in our research, have a hobbyist interest in or some other driving force encouraging us to track activity in.
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