104 Matching Annotations
  1. Last 7 days
    1. Students must have proficiency with technical databases and other resources that enable development of skills in searching the literature, including structure-based searching.

      SciFinder and Reaxys covers this

  2. Oct 2017
    1. These authors offered a link to a quiz

      This is an h. (hypothes.is link to the section of text that links to the MUST test.

      Please let me know if it does not open the confchem paper and take you to the part where the link is. ( rebelford@ualr.edu).<br> Thanks

    1. E=q1q2(4πϵ0)

      This is a public annotation of some text in LaText, which my students were annotating in the past, and messing up pages.

  3. Sep 2017
    1. eithe

      I think this needs editing

    2. Substance and Reaction Records, and these enable substances/reactions to be searched precisely in association with words/topics

      I understand what is being said here, but is this also why you can combine text and structure search? (I realize that is a different thing, but you had said SciFinder was not set up that way, and so I am wondering)

    1. Requeststhe Director-General to present to it at its 202nd session a plan of UNESCO’s participation in international celebrations of the 150th anniversary of the periodic table of chemical elements in 2019;12.EncouragesMember States to foster the mobilization of extrabudgetary contributions to UNESCO in support of the celebrations of the 150th anniversary of the periodic table of chemical elementsin 2019

      Of note

    1. The 150th anniversary of Mendeleev’s periodic table will also take place in 2019 and this would be highlight

      Note: 2019 is not only IUPAC's centenial, but the 150th anniversary of the periodic table

  4. Aug 2017
    1. NSF places high value on educating students to be leaders and innovators in emerging and rapidly changing STEM fields as well as educating a scientifically literate populace. In pursuit of this goal, IUSE: EHR supports projects that have the potential to improve student learning in STEM through development of new curricular materials and methods of instruction, and development of new assessment tools to measure student learning. I

      item 1

  5. Jul 2017
    1. dictionaries and hierarchies

      T11 I am assuming dictionaries are Compendex and Reaxys Index terms. Are there others, and what do we mean by hierarchies. Taxonomies?

    2. Let’s now go back to the initial list of options(Fig.2.2

      What is the shortcut for doing this. I can't find a breadcrumb or trail, and the back arrow does not go there. I can click Quick search, and redo the search, but there must be a better way.

    3. AND –although terms entered without any operator are interpreted as AND

      How close do the words need to be? I assume in the same document, or "record", if this is done in substance or reaction records.

    4. Summary

      I am thinking that this document should be covered first, before the structure search document. At least some aspects of this would have been useful to have covered prior to the first document (File 5)

    5. nd/orprepositions

      I am not sure what you mean by this. In the next statement you say OR, but here you say "and/or".

    6. may

      are we editing this for "American" English? I would think "can" instead of "may" is better

    7. eaxys uses severalhundred algorithms to interpret the queryand directly gives answers that may be in Document, Substanceand/or ReactionRecords

      Is there a place where further documentation on this can be found. I have Thibault's article from the ACS symposium series book, and will look this up there.

    1. and we may want to review all reactions regardless of whether yields are quoted.

      So if a yield is not reported, the planner will not show it unless you set this to zero % yield, right?

  6. Jun 2017
    1. It should be noted that this is a "bounded function", with the lower end being the melting point, and the upper end being the boiling point of a substance.  

      Damon, Ignore this....I will erase shortly, but wish to demo this functionality.

      If this is bounded between zero and 100 deg C, then how does the graph go above 100 deg C?

    1. 3.3 Initial observations of UALR student use of h. annotations concurrent with Drupal comment

      My thoughts on h.

    1. Toxicological InformationToxicological InformationHeptatoxicity

      Second try

    2. Toxicity Summary

      Use of hypothes.is in literature search, here I am linking to PubChem LCSS section on Nicotine

  7. May 2017
    1. This video shows how one could use the ability to aggregate annotations at the bottom of a page to prepare for in-class lecture.

      This video shows how hypothes.is annotations was used in flipped classroom lecture preparation.

    1.  Chemical informatics for facilitating international collaboration This activity aims at creating a working group of scientists to collaboratively source, collate, and analyse data with unique chemical signatures. It seeks to compile data collected from a broad range of routine chemical monitoring activities that contain chemical signatures (e.g. data collected from atmospheric monitoring, environmental sample collection, water testing, and more). The intent is to connect chemical and information scientists from different regions of the world to create a hub in which the information can be disseminated to the collaborators for visualisation and informative analysis of global and regional chemistry. This work is intended to facilitate engagement of the Technical Secretariat with the scientific community. Main output will be a data collation centre serving as a hub for collating and reducing data into formats compatible with the analytical tools used by the collaborating researchers. The hub, located in one of the participating universities, will support the network of collaborating scientists and build its capacity to expand beyond the implementation period.

      I believe a small EU grant has been awarded to look into this, although the funds are not available for us, we could support this, and piggy back off of it.

  8. Apr 2017
    1. e textile industry is one of the oldest and largest industries on a global level, and while dyes and pigments of natural origin have been used for coloring clothing and other purposes since 3000 BC, it is only within the past 200 years that a wide variety of synthetic dyes have begun to be produced in massive quantities.[20, 21] Textiles are classified based on the material they are made of, which in turn dictates the type of dye which is used to impart them with color; for instance, reactive, direct, and indigo dyes are used for cellulose fibers, while acid dyes are used for protein fibers and both basic and dispersed dyes are used for synthetic fibers.[22] The structures of several common dyes used for textiles, paper, foo

      dont forget to post

    1. *fulleren*

      Note, you can't use stars, but need to use the "contains" option

    2. EMTREE drug terms listed in the Index Terms

      EMTREE is like Mesh, but how do you get to the index terms, Unfortunately, h. will not link inside of Reaxys, and so I can't give a link to where I am

    1. identity search.

      For similarity search, use, https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastsimilarity_2d/cid/334/cids/txt?Threshold=95

    2. Getting molecular properties of a set of compounds

      It seems most of the things we can get are from the advanced search (entrez?) options. Can we get other items, like boiling points?

    3. https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CSCPPACGZOOCGX-UHFFFAOYSA-N/record/XML?record_type=3d

      How do you read this file? Can you pull a mol file from it?https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CSCPPACGZOOCGX-UHFFFAOYSA-N/record/XML?record_type=3d

    1. PubChem subgraph fingerprints,

      Why are these called a "Subgraph"? I see this from , wikipedia. Is it that each bit of the fingerprint represents a subgraph of the molecule, which in it self is the graph? That is, its existance/nonexistance of this subset within the entire?.

  9. Mar 2017
    1. without minor isotopes by combining the retrieved search results [from (a)] with the following Entrez indices:

      once you have done this, click on the number of hints, go to the doc sum page, go to advanced, and use the advanced query builder to perform the filters.

    2. ? [Note that a compound may have multiple EC50 values determined from different experiments (likely under different experimental conditions)

      There are two ways to get rid of duplicates. You can simply paste the CIDs into the pubchem search, and search, I think this requires Chrome.

      or

      You can go to Data/data tools in excel, and choose the "Remove duplicates" tool

    3. To perform an identity search for Cymbalta (CID 60835), go to the Chemical Structure Search pag

      so if many CIDs relate to specific isotopes, do the normal molar masses use ave values, like the periodic table?

    4. PubChem Search

      the beta search link of the homepage

    5. PubChem Chemical Structure Searc

      Direct Link is Under Services on the homepage

    1. EC50”

      Half maximal effective concentration (EC50) refers to the concentration of a drug, antibody or toxicant which induces a response halfway between the baseline and maximum after a specified exposure time

    2. s. Click the “Pharmacological Actions” link under “BioMedical Annotation” to choose the c

      Note you get 2 hits, the search 5090 and 5472495. This tells you that there is a molecule that is 80% similar and has been tested as active.

    3. n, use the smallest EC50 value (for simplicity) if there are multiple values

      Is there a quick way to recognize duplicates in Excel? In the case of CID5152, the compound CID9892481 was repeated 3 times

    4. mentioned at the top of t

      444036 is now getting 5 targets

    5. What is the difference between the non-common components of the compounds in (a)?

      Is there a quick way to compare smiles to do this?

    6. Provide the query CID in the search box and run the search. Repeat the search with the “same isoto

      note in the query, this gives #24 and #23, which in the advanced search,

      23 1:1 CovalentUnitCount

      24 56 documents

      A quick scan showed only 1 covalent unit in -24, so was -23 done just because it is good practice?

      Also, the entrez history shows here too.

      Also, in the first search with 56 results, the first three did not have isotopes specified, while in the seconds search, those were the only ones to come out. Does it always give priority in the search to ones without isotopic labels?

      This leads to a bigger question. are the molar masses from the periodic table, or are they related to specific isotopes?

    7. 2.1. The Structure Clustering tool

      Private note - useful for GHS?

    8. this URL

      Available through the services menu of PubChem homepage

    1. PDB and CSD

      PDB is biological compounds while CSD is material sciences oriented.

    2. How many compounds

      Use OR Bolean in advanced search

    3. How many compounds in

      Use "AND" of advanced search, the above classification browser results will be in search history

    4. For example, the protein-bound 3-D structure of penicillin V can be accessed via the following UR

      This can be done from PubChem TOC of Classification browser, Biomolecular Interactions and Pathways and Protein Bound 3-D Structures The next link is same, but Chemical and Physical Properties/Crystal structures

    5. ummarize what Lipinski’s rule of 5 i

      </= 5 H Bond donors </= 10 H Nond acceptors </= 500 Daltons LogP </= 5

    6. the “MeSH Synonyms” se

      This chemical has depositor supplied syntony P071 fro AK Scientific,P071

      While Cetrizine has Mesh synonym of P071

    7. zyrtec[completesynonym

      exact name match (zyrtec-D will not work, it is a partial match)

    8. t is the CID of that covalent-bonded unit? [A covalently-bound unit (or simply called covalent unit) consists of a group of

      note, two of these are mixtures, which could be filtered out by setting covalent units to 1:1

    9. The use of covalently bonded units (instead of components) removes this ambiguity because it is well accepted that NaCl is bonded through an ionic bond.)

      sodium chloride comes up with 1:2 not 1:1 covalent units.

    10. zyrtec

      gets MESH and Depositor supplied synonyms

    1. grouping

      group

    2. These conformer models aim to generate bioactive conformers,which would be found in protein-ligand complexes. For this reason, these conformers are often very different from their experimental structures determined in the gas phase

      How do you choose which are best? Both, from the perspective of creating them for the databank, and for using them as a client (in your research).

    3. following condition

      https://www.ncbi.nlm.nih.gov/pubmed/21933373 https://www.ncbi.nlm.nih.gov/pubmed/21272340 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702940/

    4. n the ST-optimization approach, the shape overlap between the molecules (that is, the ST score) are maximized and the single-point CT score is evaluated at that superposition. On the contrary, the CT-optimization considers both ST and CT scores to find the best superposition between molecules, and the single-point ST score is computed at that superposition

      Can there be some sort of superposition using an algorithm that is sort of in the middle, maximizes both ST and CT?

    5. here NAand NBare the number of bits set in the fingerprints for molecules A and B, respectively, and NABis the number of bits set in both fingerprints.

      Is there a service that generates fingerprints from smiles strings?

    6. ubChem uses its ownfingerprint called PubChem subgraph fingerprints.

      If you follow the link you see the fingerprint key, and this is confusing. How would you represent a molecule with on carbon, 1 oxygen and 2 hydrogen (formaldehyde) when the lowest C count is 2, and H count is 4

    7. choose adesireddegree of “sameness” from several predefined options. To see these options, one need to expand the options section by clicking the “plus” button next to the “option” section headin

      I get confused between indices and filters. If you open the filters, you see what I thought were Indices, (HBD,HBA,...).

      Also, what is the criteria for similar structures? I don't see a 90%, 80%,....

    8. PubChem Searc

      "Try PubChem Search Beta" from homepage

    9. PubChem Chemical

      Under Services of homepage

    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

    1. PubChem Compound:

      PubChem Indices

    2. BondChiralCount [BCC, BCCNT]: Total count of chiral bonds in a given compound, integer. BondChiralDefCount [BCDC, BCDCNT]: Total count of defined chiral bonds in a given compound, integer. BondChiralUndefCount [BCUC, BCUCNT]: Total count of undefined chiral bonds in a given compound, integer.

      I am confused on what is a chiral bond. I thought enantiomers (chiral molecules) had chiral atoms, not bonds. Are cis/trans isomers chiral bonds? If so, the boiling points are different, and enatiomers have the same boiling points, right? So what is a chiral bond?

    1. Test Account A "test" account enables you to upload data into the pending submissions database, but does not enable you to "commit" the data into the official PubChem database. The test account is just for trying the system to determine if you can successfully upload and see your structure. When you register for a test account, you must enter your e-mail address. When you go to the next screen, PubChem upload will send a message to your e-mail address with a code that you must enter on the second screen in order to proceed. This confirms the validity of the e-mail address, in order to ensure communications about your PubChem submissions. When you are read

      test account

    1. thasSOlongbeenacustomtoprefaceacourseoflectureswiththehistoryofthesciencewhichistheirsubject,thatitmaybenecessarytostate,briefly,thereasonsthathaveinducedmetodepartfromthisestablishedusage.

      This is a test of a Gutenberg Archive book uploaded to the OLCC

    1. might fail if API is not available# query common namey1 <- ci_query(c('Formaldehyde','Triclosan'), type ='name')names(y1)str(y1[['Triclosan']]) # lots of information insidey1[['Triclosan']]$inchikey# Query by CASy2 <- ci_query('50-00-0', type ='rn', match ='first')y2[['50-00-0']]$inchikey# query by inchikeyy3 <- ci_query('WSFSSNUMVMOOMR-UHFFFAOYSA-N', type ='inchikey')y3[[1]]$name# extract lop-Psapply(y1, function(y){if (length(y) == 1 && is.na(y))return(NA)y$physprop$Value[y$physprop$`Physical Property`=='log P (octanol-water)']})## End(Not ru

      this is the code but add

      Not run:

      continue with first line

    1. t the approach above is easily implemented andcan run in a wide range of environments. It has the benefitof synergy with the c

      test for public file on cheminformatics OLCC

    1. es.PubChem archives the molecular structure and bioassay data from the MLSCNand other contributors. PubChem provides search, retrieval, and data analysistools to optimize the utility of these results. PubChem further enhances the re-search utility of the

      Restricted Access Article - I am testing to see if this link works when someone is logged in, and is not logged in, to the OLCC course.

  10. Feb 2017
    1. Spelling correction

      Are mispelled words common in patents? I know someone who thinks they are done intentionally. Cheers, Bob

    1. The metadata, data, comments and any processing errors are stored in an array in PHP and then converted to XML and saved. Figures 4 and ​and55 show a comparison of the original JCAMP file (e.g. “../spectra/view/000000115/JCAMP”) and JCAMP saved in XML (e.g. “../spectra/view/000000115/XML”).

      this is to show you something

    1. ol-water partition coefficient (ClogP). The descriptors tend to convolute any different properties into these simple scalar descriptors, but can be highly effective in certain circumstances and are widely appreciated for their interpretability in interactive systems. One such set of property descriptors that has gained wide acceptance is the Lipinski rule-of-five, which has been suggested as an heuristic for indicating the oral absorption of a potential drug based on marketed orally-dosed drugs. The rule-of-five applies four calculated properties and defined cut-offs

      test of tags

    1. Morgan algorithm initially developed by Gluckat DuPont (Wilmington, DE, USA) and adapted byCAS.55

      How is the Morgan algorithm developed, and are there alternatives?

    1. Most distinctive interactions occur between vitamins and medicines curing ailments of classes such as central nervous system or dermatological in nature. Several less similar interactions filtered as distinctive, include compound pairs from distinct classes. Figure 6i,

      Note how we can use hypothes.is to link anywhere in an article, and discuss it.

    1. To automate functions on chemical data, the data structure needs to be systematically defined and consistently applied.

      Who is responsible for the systematic definitions of data structure and their consistent application?

  11. Jan 2017
    1. uick searchin Reaxysallows you to combine structure and text searches. Try doing the searc

      How do you turn on quicksearch

  12. olcc.ccce.divched.org olcc.ccce.divched.org
    1. Issues with Intelligent Search Engines

      Damon, I am not sure you are familiar with Hypothes.is, but we will be using this, and I think the first iteration of a learning assignment should be from the expert, which can then get dumbed down to multiple levels, depending on student abilities. So we can expect an iterative process.

    1. St Joseph Aspirin-Free

      S,

      Please note that a pubchem search of aspirin give acetaminophen because there is a depositor-supplied synonym called St. Joseph aspirin-free.

      I am posting this annotation public, but it could be posted to a class discussion, that sends an email to everyone in the class when the annotation is made

    1. that is, a string of 0’s and 1’s).  The position of each number in this string corresponds to a particular fragment.  If the molecule has a particular fragment,

      Do XYZ using the tanimoto coef.

    2. Molecular similarity methods can be broadly classified into two-dimensional (2-D) and three-dimensional (3-D) similarity methods.  Typically, 2-D similarity methods use so-called molecular fingerprints, which encode structural information of a molecule into a binary string (that is, a string of 0’s and 1’s).  The position of each number in this string corresponds to a particular fragment.  If the molecule has a particular fragment, t

      Using tanimoto coefficient compare the two molecules on your list

    1. Open Data in Chemistry. One can obtain all scientific data in the public domain when wanted and reuse it for whatever purpose.• Open Standards in Chemistry. One can find visible community mechanisms for protocols and communicating information. The mechanisms for creating and maintaining these standards cover a wide spectrum of human organisations, including various degrees of consent.• Open Source in Chemistry. One can use other people's code without further permission, including changing it for one's own use and distributing it again.

      Assignment 2: Relate ODOSOS to Open Notebook science in 500 words or less

      https://youtu.be/zrE_NEXmHk0

    1. BioAssays, Tested (24) Compounds identified as tested in screening experiments  BioActivity Analysis of reported tested compounds Protein 3D Structures (5) Compounds bound to proteins in atructure biology experiments Crystal Structure Of The Complex Of Goat Lactoperoxidase With Acrylonitrile At 1.98 A Resolution (1)Crystal Structure Of Thermolysin In Complex With Aniline (1)Gspb (1)... All 14 Structures BioMedical Annotation Pharmacological Actions (24) Therapeutic use and National Library of Medicine (NLM) compound classifications Carcinogens (24)Mutagens (5)Solvents (1)... All 13 Pharmacological Actions BioSystems (10) Compounds involved in biological pathways Depositor Category Chemical Vendors (24) NIH Molecular Libraries (21) Find related data Database: Select BioSystems Gene MeSH Nucleotide OMIM PMC Protein PubChem BioAssay PubChem Compound PubChem Substance PubMed Structure Taxonomy Option: Find items Search details (#4) AND 82002273[PharmActionID] Search See more... Recent activity Clear Turn Off Turn On PubChem Compounds from Classification for pchierarchy (Select 185... (907) PubChem Compounds from Classification for pchierarchy (Select 1857072)Search PubChem Compound Disciplines and Occupations Category Disciplines and Occupations Category MeSH PubChem Compounds from Classification for pchierarchy (Select 216... (2888) PubChem Compounds from Classification for pchierarchy (Select 2166072)Search PubChem Compound Your browsing activity is empty. Activity recording is turned off. Turn recording back on See more... You are here: NCBI > Chemicals & Bioassays > PubChem Compound Support Center <img alt="" src="/stat?jsdisabled=true&amp;ncbi_app=entrez&amp;ncbi_db=pccompound&amp;ncbi_pdid=docsum&amp;ncbi_phid=396C196A86FF0E210000000000D90061" />

      What are bioassays

  13. Dec 2016
    1. Builder

      When I click "All Fields" a lot of options come up, ranging from ActiceAidCount to XlogP. Are all of these Entrez indices? (some being text, and some being numerical?

      olcc

    1. ith this page you can draw a structure in 2D, compare that with its 3D structure, and also see its structural data in a variety of form

      does asprin show here

    1. Contributors can specify a ‘hold-until date’, until which the contributed data will not be visible to the public.

      On the PubChem Datasources page, there are 6 data types, https://hyp.is/G504wMLkEeafGh_HgqKgaQ/pubchem.ncbi.nlm.nih.gov/sources/

      If you go to Nature Chemical Biology, they have 9,424 live substances and 131 on hold substances.

      So does that show up twice in the above link, where there are 444 live subtance and 5 on hold substance data types?

    2. Data submission using PubChem upload

      2017 Cheminformatics OLCC students are responsible to read this section on PubChem Upload. Further information is available at the Upload Help Page, https://pubchem.ncbi.nlm.nih.gov/upload/docs/upload_help_complete.html

    1. Data TypeLive Substances(444)Live BioAssays(81)Annotations(50)On Hold BioAssays(10)Classifications(7)On Hold Substances(5)

      This is confusing. What are the onhold Substance and Bioassays? I will link to this from the article, http://nar.oxfordjournals.org/content/44/D1/D1202.long, but it seems that data submission using pubchem upload, a data source may have some data on hold, and other data live.

  14. Nov 2016
    1. Mesomerism Mesomerism is the concept related to the situation in which the molecular structure cannot be unambiguously represented by a single classical structural formula; rather, two (or more) mesomeric structures must be drawn and considered to contribute to the overall picture. As the IUPAC Gold Book states, “mesomerism” is “Essentially synonymous with resonance. The term is particularly associated with the picture of π-electrons as less localized in an actual molecule than in a Lewis formula. The term is intended to imply that the correct representation of a structure is intermediate between two or more Lewis formulae” [28]. In other words, mesomers are considered as imaginary objects (or even drawing artifacts) that cannot be distinguished by a simple chemical identifier. Mesomerism is effectively eliminated in InChI. Mesomers have the same InChIs (this is true for all possible InChI layouts of layers). Actually, this is very natural. Mesomeric structures of a molecular entity have the same basic connectivity but differ in bond orders, and maybe by having atomic charges on different atoms. InChI does not use bond orders and does not place charges on particular atoms; the placement of hydrogen atoms in a mesomeric system, which would be important for InChI, is always the same.

      In class yesterday we covered mesomerism with canonical SMILES, tomorrow you need to be prepared to explain how InChI covers this for the molecule you used in class yesterday, and be prepared to lead a discussion with your group on the differences between the two methods.

    1. GHS Classification

      Class, in section 12.1.1 you see the GHS safety codes for acetone and at the bottom of this section you get links to original sources. These include the International Labor Organization, European Union, HSIS of Australia and the Japanese National Institute of Technology. Your assignment is to compare these four sources of GHS Hazard Statements for Acetone, and be prepared for an in-class discussion on OSHA's Hazcom 2012, https://www.osha.gov/dsg/hazcom/ghs-final-rule.html and specifically appendix c https://www.osha.gov/dsg/hazcom/appendix_c.pdf

    1. Smallest number indicates limiting reagent.

      You are half way through the mole-to-mole step, where you would place on the numerator the stioichiometric coefficient of the compound you want to solve for.