34 Matching Annotations
  1. Mar 2017
    1. f the query is a phrase or a name with non-alphanumeric characters, double quotes should be used around the query. 

      text searches with numbers, should use double quotes

    2. http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pccompound (for Compound) http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pcsubstance (for Substance) http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pcassay (for BioAssay).  

      These links are the same as the above section on indices

    3. retrieved in the XML format, using the eInfo functionality in E-Utilities (which will be covered in Module 7):

      to open these xml files in Google sheets use: =importxml(A1,"//Field/FullName") where in A1 you place the link below

    4. For numeric indices, a search for a range of values can be done by using minimum and maximum values separated by a colon and followed by the bracketed index name (e.g., “100:105[MolecularWeight]”).

      use of numeric indices X:Y

    5. FLink tool

      The flink tool is also useful for 3D structure, macromolecular structure search. https://goo.gl/tgS4QB Amita

    6. However, some special filters, such as the "lipinski rule of 5" filter, or the “all” filter, are not link-based.

      What is "lipnski rule of 5" filter and why is it not link based? Amita

    7. The Entrez Search and Retrieval System

      This link provided here gives detail about Entrez, how it works. http://www.ncbi.nlm.nih.gov/books/NBK184582/ Amita

    8. In practice, the identifier exchange service may be used as a quick approach to search the PubChem Compound database using multiple queries, although this type of task may be performed programmatically (for example, using PUG-REST,10 which will be discussed in Module 7).

      since pug rest query can be used as a quick approach to search the pubchem compounds. can I also use it to get the list of all pubchem IDs, if yes pls how?.(nwume)

    9. 3.2. Identifier Exchange Service

      Can this service be accessed by other methods instead of using the form?


    10. “[synonym]” index returns additional 97 compounds. 

      i noticed that when i search Aspirin[synonym] i get 97 hits but if i search Aspirin[synonyms] i get 102 hits which is the same number "aspirin" gave me. can someone explain why its like that, because i thought it will give me the same number of hits as aspirin[synonym] (.Nwume)

    11. MeSH Synonyms

      Why are some of the MeSH synonyms not the same as the depositor-provided synonyms Emily

    12. 1.2.6. Entrez History

      Is there a way for Entrez to save my search history permanently? -Phuc

    13. Entrez links are cross links or associations between records in different Entrez databases, or within the same database.  These links may be applied to an entire search result list (via the “find related data” section at the right column of a DocSum page) or to an individual record (via links at the bottom of each record presented on the DocSum page).  The Entrez links provide a way to discover relevant information in other Entrez databases based on a user’s specific interests.  Equivalently, one may think of this as a way to transform an identifier list from one database to another based on a particular criterion. Note that there are limits to how many records may be used as input in a link operation.  To process a large amount of input records and/or to expect a large amount of output records associated with the input records, one should use the FLink tool (https://www.ncbi.nlm.nih.gov/Structure/flink/flink.cgi).         A complete list of the Entrez links available for the three PubChem databases can be retrieved in the XML format through these links http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pccompound (for Compound) http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pcsubstance (for Substance) http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pcassay (for BioAssay).  

      what is XML format, and how can it be applied? Esther

    14. MeSH (Medical Subject Headings)

      Is there a difference between the National Library of Medicine MeSH and this MeSH? I was confused when reading and found out that there are two sections where it is discussed. Under Synonym and under classification. Daniel

    1. why the “legacy” designation was introduced in PubChem

      :…. Pubchem does not allow anyone other than the data contributor to modify the provided information and that makes some of the records in PubChem persist with outdated or incorrect data. so in other to help correct this the “legacy” designation was introduced.(nwume)

    1. Synonyms

      please can someone give me a clear difference between a MeSH synonym and a depositor-supplied synonym (nwume)

    1. BioAssay classification tool

      the bioassay clasificational tools are available at this link https://goo.gl/3jYFXA and this link https://goo.gl/JcGyLf so you can check the tools and find out how to use them.(nwume)

    1. Cameo ChemicalsResearch and Development, Governmental Organizations, Curation Efforts

      I am pretty familiar with the software that CAMEO Chemicals puts out that we use in emergency response but had no idea they also provided data to services like PubChem.


    1. The listed chemicals are safer alternatives, grouped by their functional-use class.

      There are quite a few safer alternatives in this list, but none are listed on the PubCHem page under the EPA Safer Choice Label for Use and Manufacturing on the PubChem Classification Browser which links itself to this page.


    1. The input list can be provided by text, a file, or Entrez history. Registry IDs, SIDs, CIDs, InChIKey, and SMILES can be separated by white space, comma, tab, or carriage return, however InChI and Synonyms should be separated by tab or carriage return only. If Registry IDs are provided, the Registry Source Name must also be provided.

      This says that an input list can be provided by a file. What types of files would work? CSV, XML, etc? Also is there a limit to how many identifiers can be in a single exchange?

    1. Lead-like

      This is also called Congreve’s rule of 3. For those having trouble finding it, also see the link at top of page for rule of three. Emily

    2. Components of the rule

      This gives the actual guide lines however use this webpage for a easier way to read them. https://goo.gl/Wjl7Sm Emily

    3. Rule of five" redirects here. For the rule of thumb as it applies to the C++11 programming language, see Rule of three (C++ programming). Lipinski's rule of five also known as the Pfizer's rule of five or simply the Rule of five (RO5) is a rule of thumb to evaluate druglikeness or determine if a chemical compound with a certain pharmacological or biological activity has properties that would make it a likely orally active drug in humans. The rule was formulated by Christopher A. Lipinski in 1997, based on the observation that most orally administered drugs are relatively small and moderately lipophilic molecules.[1][2] The rule describes molecular properties important for a drug's pharmacokinetics in the human body, including their absorption, distribution, metabolism, and excretion ("ADME"). However, the rule does not predict if a compound is pharmacologically active.

      what is the significance of Lipinski's rule of five in Pharmaceutical field? Esther

    4. Partition coefficient log P in −0.4 to +5.6 range

      Due to the extension because of improvement in druglikeness, for partition coefficient do we stick with the range of not greater than 5, or 5.6. Daniel

    1. In analogy to the rule of five, it has been proposed that ideal fragments should follow the 'rule of three' (molecular weight < 300, ClogP < 3, the number of hydrogen bond donors and acceptors each should be < 3 and the number of rotatable bonds should be < 3).[1] Since the fragments have relatively low affinity for their targets, they must have high water solubility so that they can be screened at higher concentrations.

      This is a great description of what Congreve’s rule of 3 actually consists of. Emily

    1. Entrez Nodes Are Intended for Linking

      Can this also be used to link chemical to reactions from research projects that use them? Emily

    2. An Entrez "node" is a collection of data that is grouped together and indexed together

      As an example for searching on Entrez AIDS so like Literature, Health, Genomes, etc are considered as a "node" and little section above that are link within nodes?- Phuc

    3. For example, a well-annotated SWISS-PROT record for a particular protein may have fields that describe other protein or GenBank records from which it was derived.

      From this article on Entrez, is SWISS-PROT record for proteins gotten from GenBank? Daniel

    1. Biomolecular Interactions and Pathways

      This link should helped answering part of question 3 -Phuc

    1. wwPDB data centers serve as deposition, annotation, and distribution sites of the PDB archive. Each site offers tools for searching, visualizing, and analyzing PDB data. PDBe Protein Data Bank in Europe Rich information about all PDB entries, multiple search and browse facilities, advanced services including PDBePISA, PDBeFold and PDBeMotif, advanced visualisation and validation of NMR and EM structures, tools for bioinformaticians.

      How can i search for PDB entries of a protein with specific Swiss-Prot ID


    2. Since 1971, the Protein Data Bank archive (PDB) has served as the single repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies. The Worldwide PDB (wwPDB) organization manages the PDB archive and ensures that the PDB is freely and publicly available to the global community. Learn more about PDB HISTORY and FUTURE.

      Are there any copyright restrictions to use images or data on PDB website?


    1. DrugBank CAMEO Chemicals The National Institute for Occupational Safety and Health - NIOSH HSDB ILO-ICSC Human Metabolome Database OSHA Chemical Sampling Information OSHA Occupational Chemical DB NIOSH-PocketGuide

      Is this all the information needed for when we do a PUG-REST request? Daniel

    1. The E-utilities are therefore the structured interface to the Entrez system

      In other words Entrez database system relies on E-Utilities. Daniel