Hi everyone,
I was having trouble on this module about what the difference between data provenance and substance records. Dr. Kim said that the substance records are not the data provenance, however they do contain the data provenance information. I hope this helps any that where confused like I was. Link for hypothesis (<a href="https://goo.gl/o3f9L6">https://goo.gl/o3f9L6</a>)
Emily
Discussion
more information on ChEmBL
On careful study of Chemical databases, i want to know how i can easily identify or site ChEMBL when being used in a publication?
Esther.
Covalently-bonded unit
I'm still a bit confused with covalently-bonded unit (CBU)... I did a small search and methanol has CBU of 1 and if I look for zyrtec which is Cetirizine dihydrochloride has CBU of 3. Does that mean covalently-bonded unit indicate how many species are there in a compound? -Phuc
Extra Reading
Hi Dr. Kim
While waiting for more participants in this project, do you have any suggested paper regarding of 3-D similarity? I want to study the background before the project started. Thanks- Phuc
Welcome!
Hello Lyndsie! Damon is currently traveling, so I am taking the liberty of responding to your comment. First off, I am glad you are interested in this project and am particularly excited about your suggestion to "merge" this topic with the project on information literacy. I think that approach will be very interesting and I would very much enjoy working with you on such a project. I think that at this point, we should see who else joins the project (whether this one or Project 1) and then we can "sit down" with Damon and others who join to hash out different sub-projects that people can work on individually or in groups.Cheers,Anja
PubChem and ChEMBL
In reading about Bioactivity data in PubChem, i came about a question about the relation between PubChem and ChEMBL. Mr Kim actually helped me understand the relation between the two. So from what i can get ,depending on the scientific question needed to be answered, we can determine if PubChem or ChEMBL is appropriate.
.<a href="https://goo.gl/016mlo">https://goo.gl/016mlo</a>.
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Cheers,
Conceptually, covalently-bonded units are components of a compound. Some compound records in PubChem are mixtures or salts, which consist of multiple components, and the concept of covalently-bonded units is used to define the number of components in a compound in PubChem.
Suppose that you have two compounds, CH3COONa (sodium acetate) and CH3COOH (acetic acid). In sodium acetate, the bond between the sodium and oxygen atoms are ionic, so sodium acetate has two covalently-bonded units (sodium and acetate). (Although the sodium atom is not covalently bonded to anything, it is counted as one covalently-bonded unit.) For acetic acid, the H atom of the carboxylic acid group is covalently bonded to the oxygen atom, so acetic acid has one covalently-bonded unit. As another example, the only bond in NaCl is the ionic bond between the Na and Cl atoms, so this compound has two covalently-bonded units.
In your example, all atoms in methanol are connected with covalent bonds, you can view as one covalently-bonded unit (component). However, cetirizine dihydrochloride has three covalently-bonded units (one cetirizine and two hydrochloride). No covalent bonds are formed *between* these three components, so each of them is viewed as a covalent-bonded unit.