Methods

 

 

 

 

1.0 ACH Methods Database

 

  • Analyze Chemicals (ACH) Methods is one of the world's first open source crowdsourced chemical analysis methods database very similar to  MethodsNow by CAS.

     

  • Click here to view the ACH method for Malvidin, a flavanoid polyphenol belonging to anthrocyanin subclass. Click here to download a .odt version (open office XML based word processing format, compatible with word processors like MS Word).

     

  • We unlock and compile the protocols and methods hidden away in government reports, thesis/dissertations, peer-reviewed papers and other scholarly works, laboratory notebooks etc. While many of these documents are converted into pdf and available online, the problem is that OCR is seldom without errors and text searching these files directly is still a problem. Hence we have to rely on our volunteers to manually curate these data and convert them into useful formats so they become widely available. We are also working with IBM Watson Knowledge Studio to develop AI solutions to automate this process and initial results have been encouraging.

 

 

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2.0 Scope

 

The following types are within the scope of the ACH Methods database:

     

  • Methods developed by us in house over the years for our clients, subject to obtaining their explicit written approval.

  • Methods and data in public domain from expired patents as well as existing and draft EPA, FDA, EFSA methods. As part of ongoing development work, we are going to make API calls to other complementary databases so that we can have seamless user experience without any replication of effort.

  • Methods contributed by our partners in chemical industry, non profit groups, federal, state and local  labs and agencies based on their in house SOPs. We work closely with our partners to ensure that all the proprietary information has been removed, and the method made as general as possible.

  • Methods/data contributed by industry and academic ACH users from their own published peer-reviewed papers, thesis, laboratory notebooks etc. These methods are reviewed by a moderator before they are publicly available on the ACH database.

  • Methods based on modification of existing literature method, typically for the purpose of simplifying them, or reducing the cost of the method. These are typically contributed by expert ACH volunteers and reviewed by a moderator before they are made publicly available on the ACH database.

 

 

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3.0 Call for contributions

 

Did you recently published a paper, and you couldn’t fit everything in the methods section and Supporting info? we would be very excited to host that here on ACH.

 

Do you have tons of raw data files from kinetics experiments which didnt make it to the paper/SI?  we would love to put it on ACH so these become more widely available for meta analysis and data mining without the constraints of copyrights and restrictions placed on it by publishers such as Elsevier, Wiley etc.

 

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4.0 Submit New Chemical

 

Please click here to submit a chemical or degradation/metabolism analysis method or its related experimental data.

 

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5.0 Contributor/Author Guide

 

Our database is intended to be not just human readable, but also parse-able by text mining programs. Hence, we prefer contributions to follow a general guideline.

 

  • Please go here to draw the structure of the chemical you wish to contribute to our database. You can also enter the common chemical name, SMILES, IUPAC name, CAS number etc in the enter Chemical Identifier box as shown in figure 5.1.

 

Fig 5.1: Enter Chemical Identifier box with generation of InChiKey

 

 

  • InChiKey are set of unique text strings to depict each chemical so they are more readily machine searchable. We suggest that contributors first run a search of a chemical they wish to contribute before creating a new entry; if they find the chemical already in the database than the user should refer to the workflow to add new method to the existing entry via the edit button.

     

  • We are using National Cancer Institute's chemical identifier resolver web services to generate InChiKey, so users can check that out here in case they need to find identifiers other than InChiKey.

     

  • SMILES strings can be generated from NCI link mentioned above or from any of the chemical drawing programs like MarvinSketch, ChemDraw JChemPaint etc. The last one is free and open source and is recommended by ACH. It can be downloaded from here.

     

  • Even though pdf files are the standard for publishing in scientific community, its actually a terrible format when it comes to make documents machine readable. An easy way to test this issue is to copy a pdf file, and paste it in notepad to convert it to .txt; A much better file format is .txt, which is very universal, xml, or even .doc,.odt etc. Hence We would really discourage potential contributors from submitting a file in pdf format. However, we are still going to allow pdf submissions for near future; however we ask that the contributor also email us at support@analyzechemicals.com so that we can work with them in case we run into issues to incorporate it in the database.

     

  • The drop down selection available for method/data type (Fig 5.2) is based on the primary instrumental technique used. Please mention in notes in case of selecting “other”. We are going to update the section to add GC-MS and LC-MS in the next version and we welcome comments and suggestions if you think we need to add other specific instrumental types. The selections currently available are:

     

    • UV-VIS: UV-VIS spectrometer

    • GC: Gas chromatography

    • HPLC: High performance liquid chromatography

    • TLC: thin layer chromatography

    • PC: paper chromatography

    • CE: Capilary electrophoresis

    • Other

 

Fig: 5.2: Chemical Analysis: Methods section of the new chemical submission form

 

  • We also accept protocols and related experimental data specifically geared towards determining degradation/metabolism products of chemicals from processes such as abiotic hydrolysis, aerobic biodegradation, abiotic reduction, anaerobic biodegradation, photolysis, oxidation etc. We suggest that the contributor mention the predominant type of processes the protocol is designed for in the notes section itself, as shown in figure 5.2.

 

 

Fig 5.2: Degradation/Metabolism analysis section of the new chemical submission form

 

  • Please also mention the type of the method in notes as defined in the 2.0 scope section. For example, if you are contributing a new method and data from your own paper, than its a 2.0(IV) type method. However, if it is a modification of an existing method, than its a 2.0 (V) type. We just need this information so we can review it without any delays. In case of overlapping subtypes (as in cases of IV and V), please put it as 2.0(V).

 

 

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