ChEBI in Bioclipse

Says it all, really.

The scrolling can hang if you move too fast, which might be due to garbage collection? It is a very large file....

Comments

How large is the file? Can I download it somewhere? Should we set up a ChEBI plugin, perhaps? Or maybe have this ChEBI data as data plugin? That would be easiest...

26 April 2009 at 09:32

gilleain said…

1) 58.2 Mb
2) From the ebi ftp site - I /think/ the ChEBI team meant it to be public, but I will ask them
3) Probably not, they have a good website for this purpose.
4) Maybe, but again, depending on the team.

It is a nice test for bioclipse, but there are other similar tests, in a way.

26 April 2009 at 11:17

Kirill said…

Re. (2): It should appear on ftp next Wednesday (April ChEBI release).

26 April 2009 at 20:33

Kirill said…

Check ftp://ftp.ebi.ac.uk/pub/databases/chebi/SDF/. The data is provided in two flavours:
* Chebi_lite.sdf file contains only the chemical structure, ChEBI identifier and ChEBI Name.
* Chebi_complete.sdf file contains all the chemical structures and associated information.

29 April 2009 at 18:30

chalky

I wanted to show something that hints at the things that the new architecture can afford us: This is using a Java2D graphics Paint object to make it look like chalk...kindof. It's a very simplistic way of doing it by making a small image with a random number of white, gray, lightgray, and black pixels. edit: it doesn't look so good at small scales some tweaking of stroke widths and so on is essential.

1,2-dichlorocyclopropane and a spiran

As I am reading a book called "Symmetry in Chemistry" (H. H. Jaffé and M. Orchin) I thought I would try out a couple of examples that they use. One is 1,2-dichlorocylopropane : which is, apparently, dissymmetric because it has a symmetry element (a C2 axis) but is optically active. Incidentally, wedges can look horrible in small structures - this is why: The box around the hydrogen is shaded in grey, to show the effect of overlap. A possible fix might be to shorten the wedge, but sadly this would require working out the bounds of the text when calculating the wedge, which has to be done at render time. Oh well. Another interesting example is this 'spiran', which I can't find on ChEBI or ChemSpider: Image again courtesy of JChempaint . I guess the problem marker (the red line) on the N suggests that it is not a real compound? In any case, some simple code to determine potential chiral centres (using signatures) finds 2 in the cyclopropane structure, and 4 in the ...

Adamantane, Diamantane, Twistane

After cubane, the thought occurred to look at other regular hydrocarbons. If only there was some sort of classification of chemicals that I could use look up similar structures. Oh wate, there is . Anyway, adamantane is not as regular as cubane, but it is highly symmetrical, looking like three cyclohexanes fused together. The vertices fall into two different types when colored by signature: The carbons with three carbon neighbours (degree-3, in the simple graph) have signature (a) and the degree-2 carbons have signature (b). Atoms of one type are only connected to atoms of another - the graph is bipartite . Adamantane connects together to form diamondoids (or, rather, this class have adamantane as a repeating subunit). One such is diamantane , which is no longer bipartite when colored by signature: It has three classes of vertex in the simple graph (a and b), as the set with degree-3 has been split in two. The tree for signature (c) is not shown. The graph is still bipartite accordin...

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