AKos
Consulting & Solutions GmbH
a chemoinformatics company

 

 


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  1. What can you do with iScienceSearch ?

  2. What makes iScienceSearch unique?

  3. What does ‘federated search’ mean?

  4.    What is the advantage of a federated search compared with building databases?

  5.    How big is the ‘problem’ of not finding links to curated databases in systems such as ChemSpider or PubChem?

  6.    Is that a problem for only ‘special’ compound cases?

  7.    Is this a general problem that curated databases have a great time lag of updating?

  8. How up-to-date is Google in respect to e.g. PubChem records?

  9. Does scientists get  the most recent information on the internet?

  10. What means ‘crosslinking’ or ‘extended’ search in iScienceSearch ?

  11.    What means ‘structure query’ in the context of iScienceSearch ?

  12. Can you submit more than one structure query at a time?

  13.    Can you submit more than one query at a time?

  14.    Do you support formats other than single structure and SDFile?

  15. Can you search for reaction methodologies?

  16. Can you search for compounds and their biological effects?

  17.    Why have we integrated PASS?

  18. Can you predict other properties?

  19. Can you search for structure modified proteins?

  20.    How do you search with proteins and peptides?

  21. Text vs structure search

  22. Can you search over REAXYS?

  23. Does iScienceSearch work on an iPad or smart phone?

  24.    Does iScienceSearch support  both PC and Macintosh?

  25. Can on compare iScienceSearch with SCiFinder?


  1. What can you do with iScienceSearch ?
    iScienceSearch allows searching currently more than 86 free chemistry databases and scientific journals on the internet by structure, CAS Registry Number, names, synonyms,  and free text.

  2. What makes iScienceSearch unique?
    iScienceSearch is the only search engine for scientists performing a true federated search over all major chemistry databases and scientific journals, and you can search by chemical strucutre.

  3. What does ‘federated search’ mean?
    Federated search is an information retrieval technology that allows the simultaneous search of multiple searchable resources. A user makes a single query request which is distributed to the search engines participating in the federation. The federated search then aggregates the results that are received from the search engines for presentation to the user. (see
    http://en.wikipedia.org/wiki/Federated_search)
    Most searches as in ChemSpider, PuChem, etc. use a database or go over an index as in Google.
    iScienceSearch uses Web API’s or web services exposed by the various data sources included in iScienceSearch and searches all these data sources independent from each other. That means a given search in a given data source in iScienceSearch is always using the most current version of the data source for the search.

  4. What is the advantage of a federated search compared with building databases?
    You get the most current snapshot of a data source using federated search. A data source aggregator such a ChemSpider needs to update the database. The earliest a newly added record shows up in a given curated data source is when the owner of the database provides an update and this update is processed by the data aggregator.
    In a federated search, all data sources are searched independent from each other and the search always uses the most current version of the data source. Means, as soon a new record is added to a given database, this record can be found.

  5. How big is the ‘problem’ of not finding links to curated databases in systems such as ChemSpider or PubChem?
    It would be a fair assumption that practically every compound in ChemSpider is also contained in the PubChem databases and vice versa. Reality is PubChem currently only references 50% of the ChemSpider records and ChemSpider only references 20% of the PubChem references. 

  6. Is that a problem for only ‘special’ compound cases?
    Not at all! Take as example ‘Catechol’ (2-Hydroxyphenole), a very simple compound. Of course this compound is present in both the PubChem database and in the ChemSpider database. But there is no link to the corresponding record in the PubChem database in ChemSpider and there is also no reference to the Catechol record in the PubChem database. This means you don’t find safety data if you look only in ChemSpider.

  7. Is this a general problem that curated databases have a great time lag of updating?
    Open this link  http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pcsubstance&term=all[filt]
    This link shows the most recently added records to the PubChem database. Take the first record and check if you find a link to this record in the ChemSpider database. It is more or less guaranteed that you will not find that link. Browse a couple (if you like a couple of hundred) pages to look at other recently added (but not most recently) added records. The chance is still extremely high that you will not find that link in the ChemSpider database.

  8. How up-to-date is Google in respect to e.g. PubChem records?
    Use the above link and look up the most recently added compound and try to locate that record via a Google search (e.g. using the name). Like in the case of ChemSpider is very unlikely that you will find that record. A newly added record to a Website shows up in Google when the Google index gets updated with the most current snapshot of the website. This update frequency is mostly dependent on how frequent a site is used. It is easy to imagine that PubChem, a scientific database and never will be accessed as frequently as e.g. sites such as YouTube. The update  frequency will be rather low.

  9. Does scientists get  the most recent information on the internet?
    No, not if you use Google. If you want to find the most recently added information in all databases on the Internet you either have to use the native user interfaces of all those databases, which of course means you have to know the URLs of all those databases and you have to know how to use those native user interfaces or you use iScienceSearch. This provides a single user interface for all those databases. You do not need to know the URLs of those databases and you always search the most current version of the databases. Try it out, and search for "biodegradable delivery" in Google and for instance in PubMed. Google ranks hits by its own algorithm, PubMed gives you the latest reference first. This seems to be sensible for science

  10. What means ‘extended’ search in iScienceSearch ?
    For every chemistry related query i.e. either a chemical structure, or a CAS Registry number or a chemical name we try to retrieve both the structure, CAS Registry number and other chemical names (synonyms, trivial names, brand names, IUPAC names). We include automatically all this information in the final query. That means, if you type ‘Catechol’ in the textbox of the iScienceSearch start page and click on ‘Search for safety information’, we try to find the CAS Registry number for catechol, the chemical structure of Catechol, and additional names. If this step is completed we search safety databases on the internet by structure, CAS Registry number and name. This ‘extension’ of the original query is pretty useful, since not all databases containing safety information support, for example structure searches, but the very most do support searches by CAS Registry number and/or chemical name.

  11. What means ‘structure query’ in the context of iScienceSearch ?
    Since we automatically search for structure, name, and CAS Registry Number if possible, when you enter a name, structure or CAS Registry Number, a structure query means more than only searching by chemical structure.

  12. Can you submit more than one structure query at a time?
    iScienceSearch will support SDFile input in a future version. We had this is in the previous version, known under CWM Global Search. That means you can read in a SDFile containing several structures and search all of the contained structures on the internet. Like we do for single structure queries, we also lookup CAS numbers for every structure in the SDFile and automatically extend the internet search using those CAS Registry numbers.

  13. Can you submit more than one query at a time?
    No, each query will at least give you answers from the first part of the search. You always should click "Search more data sources". This will go on in the background. You can already work with the result page.

  14. Do you support formats other than single structure and SDFile?
    iScienceSearch will allow in future RDFiles. You can draw or paste (by dragging) a reaction in the structure box. We split the reaction into the various members (reactants, reagents and products) and search those structures on the internet. That means you can search for commercial suppliers and safety information for all reactants in one go.  Also for structures from reactions we extend the search with CAS Registry numbers, and names if those can be found. We even support RDFile input i.e. you can search more than one reaction with a single click.

  15. Can you search for reaction methodologies?
    Not really, we do not search for reactions, only for structures.

  16. Can you search for compounds and their biological effects?
    You can start a structure query ( by now you know that a structure query means searching by structure, CAS registry Number and name) searching over ‘Drug Information’.  If you start with a text string, i.e. ‘rheumatoid arthritis’ and you search over ‘Chemical Databases’ you will get quickly small molecules with the desired biological activity.

  17. Why have we integrated PASS?
    There is no system that shows all biological effects of compounds. PASS predicts over 4000 effects. We have integrated this prediction tool for single compounds. If you process large SDFiles you can purchase the program PASS from AKos GmbH.

  18. Can you predict other properties?
    With the tool ´"Property Prediction" you will get calculated physical properties. You also will see links to other datasources that provide calculated and even experimental physical properties. Additional prperties can be calculated with 'chemicalize', the property prediction tool from ChemAxon. It gives logP, rotatable bonds, rule of five, and much, much more.

  19. Can you search for structure modified proteins?
    There are many structure modified proteins on the Internet. But the drawing of those structures is cumbersome. For this we have integrated Proteax "Search peptides", see below.

  20. How do you search with proteins and peptides?
    We have integrated Proteax. Proteax is a simple to use Peptide/Protein editor that helps you to generate chemical structures by input of one or three letter codes. With a click you generate the full structure. You can edit this further in the editor. The generated structure can be searched in databases such as PubChem, CheEBI , Drugbank etc., including the possibility to perform substructure searches and structure similarity searches.

  21. Text vs structure search
    You can by any names, or text. You should be aware that the different search engines have their own way of interpreting text strings. Sometimes they ignore numbers, and hyphens, create separate strings and give you unspecific results. A good idea is to use the menu button "Find structure for chemical name" and transform you name into a structure. Afterwards you have to clear the text box. A search with the structure is faster and more accurate.

  22. Can you search over REAXYS?
    For organizations that have a license for REAXYS, we have integrated the possibility to execute a REAXYS search from the iScienceSearch user interface.

  23. Does iScienceSearch work on an iPad or smart phone?
    Yes.

  24. Does iScienceSearch support  both PC and Macintosh?
    Yes, we support all major browsers ,Internet Explorer, Firefox, Chrome, Safari on both Windows and Macintosh (MacOS).

  25. Can one compare iScienceSearch with SciFinder?
    iScienceSearch should not be compared to SciFinder, and if you look at the price this is pretty obvious. You will find many answers either with iScienceSearch or SciFinder, and an experienced user will know when to start his search in SciFinder and when in iScienceSearch . If you want to make a comprehensive search, you probably cannot ignore the Internet any longer. We have enough examples showing that structures ar enot in SciFinder, or references not linked to the structures. If you don't find anything suitable in SciFinder it is probably a good idea to start iScienceSearch .