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Frequently Asked Question (Registration & LogIn related)

  1. How to Register to get Screen name & Password for OSDDChem Login ?

    Ans. Please follow the link: Click Here

  2. Forgot Password ?

    Ans. Please follow the link: Click Here

  3. Problem proposing / uploading molecules ?

    Ans. Please contact at: info@osdd.net

Frequently Asked Questions (Compound Submission Related)

  1. Users who have SDF and MOL files can use them for submission. Users who have SMILES of the molecules can use them to generate the structures, SDF and MOL formats and then use them for making submissions. In case, the users do not have SMILES/SDF or MOL files they can draw the structures using the JME applet provided under submission menu and generate SMILES /SDF and MOL files and then use them for submission.

  2. In this beta version it is possible to submit and download single molecules using the available options. For Bulk submission and download of data kindly contact info@osdd.net

  3. What is the purpose of OSDDChem chemical database?
    Ans. OSDDChem chemical database is an open repository of information on synthesised, semi-synthesized, natural and virtually designed molecules from the OSDD community. OSDDChem is aimed to contain both known molecules, predicted structures for synthesis and novel compounds that can be screened against tropical diseases like TB and Malaria

  4. Who can contribute to the database?
    Ans. Any researcher/scientist/professor/graduate or under graduate student who wishes to contribute a molecule-synthesised ,semi-synthesized, natural or virtually designed and who is willing to make the data and results open on OSDD portal can contribute to the database.

  5. What molecules can be submitted in the database?
    Ans. Any synthesised, semi-synthesized, natural or virtually designed molecule can be submitted to the database. In case of synthesized/semi-symthesized/natural molecules the submissions should be supported by Spectroscopic /NMR/HPLC characterisation and the compounds should posses 90% purity

  6. What is the procedure to submit - single molecule, batch of molecules?
    Users have to be a member of OSDD and have to log in using the Sysborg screen name .Once logged in, users can follow the submission link and reach the OSDDChem Data submission page and submit the molecules by filling the details
    * Users who have the SMILES format but not the SDF/MOL files can generate the same using the JME applet using SMILES as input. Similarly users who don't have the SMILES notation can generate SMILES / SDF/ MOL formats by manually drawing and submitting the structures using JME applet.
    * Being the beta version, submission of only single molecules have been made possible. For Batch submission kindly contact info@osdd.net

  7. Will OSDD screen the molecules?
    Ans. In the first phase, OSDD will screen the molecules against TB. This will be extended to Malaria in the second phase. The screening data will be made available to the community. The contributors can use the screening data to publish papers, make presentations, posters etc. In such cases, the contributors should acknowledge the OSDD consortium by adding it as a co author in all publications coming out of this work.
    Some journals require address and email of all co authors. In the case of OSDD Consortium, the address will be Council of Scientific and Industrial Research, Anusandhan Bhavan, 2 Rafi Marg, New Delhi -110001. And email is info@osdd.net

  8. Should I be a registered OSDD member to be able use the OSDDChem?
    Ans. Yes, anyone who wishes to access or contribute to the database need to be a registered member of OSDD and should have a valid Sysborg username and password.

  9. How will my contribution be acknowledged or rewarded?
    Ans. OSDD believes that attribution is the greatest reward of science. OSDD follows a micro attribution policy, where each contribution is attributed to the respective individual contributor. The contributions are made available in the open portal and is reflected against the name of the contributor. Others using this information need to cite and credit the existing information. In this way each contributor is assured of the right of attribution.
    All the users and contributions are subject to OSDD sign in license which all community members have to adhere to. It treats the entire information available on the portal as .protected collective information. It mandates common ownership of the data and research results, sharing of such data, contribute back of improvements to the protected collective information. Such Protected Collective Information is held on behalf of OSDD community by CSIR as a trustee holder with legal powers and authority for legal action. OSDD ensures that all contributions made on OSDD are attributed to the contributors. If individual researchers would like to patent their inventions for this purpose, they are welcome to do so. In such cases, OSDD will have to be given a worldwide, royalty free, non exclusive licence to work further and develop drugs. OSDD will take forward such molecules in the drug discovery pipeline and make it available without IP encumbrances in the developing world.
    The individual contributors can recoup the expenditure incurred in making the molecules by posting the project on Sysborg 2.0 and getting it reviewed by the community

  10. Can I submit unpublished data?
    Ans. Yes. Users are welcome to submit unpublished data. In such cases the screening results are made available to community and the contributors has the freedom to publish the results acknowledging OSDD consortium as the co-author.

  11. What are the mandatory requirements for submission?
    Ans.* The submissions should be supported by SDF/MOL files *The synthesised/semi-synthesised/natural compounds should be submitted along with their spectroscopic/NMR/HPLC data *The synthesized/ The synthesised/semi-synthesised/natural compounds should be 90% pure *Wherever possible, an IP search should be done and the result should be made available

  12. Can we use this data for screening for our personal research?
    Ans. The screening data may be used for further research. However, you are required to contribute the improvements back to the community by depositing the research data of the improvements. The OSDD community expects you to acknowledge the community wherever its work is used.

  13. For further help please contact : osddhelpdesk (skype Id )

JME Help (Draw/Upload molecules)

Q.1. How to Draw Molecule ?
Ans. Please follow the link: Help

Q.2. What do the symbols denote in JME Window ?
Ans.

Q.3. Why is shown in top left of JME Window ?
Ans. After a structure is drawn with the JME editor, the SMILES string is obtained by clicking on the smiley face, . A small window will pop-up and display the SMILES string. This string can then be copied and pasted into another location.



Figure: Description of buttons used to draw Molcule with JME molecular editor




 
Developed by Arun Sharma (IMTECH),  Biju Surya (MCC Open Lab.)