Instructions to Upload Screening

and CMP Activity Data

Content

  1. Introduction
  2. User Registration
  3. Upload Steps

    1. Name-Value Syntax
    2. Screen Annotations
    3. Compound Annotations
  4. Screening History of Compounds
  5. Accessing Screening Data
  6. Editing of Uploaded Information
  7. Troubleshooting
  8. Help Us to Improve this Service

  1. Introduction

    2. The screening database component of ChemMine is a versatile publication and management system for diverse compound bioactivity and screening data. External and internal users can upload their data via a web browser. The interactive interface allows the screen 'owners' to modify and expand their deposited bioactivity data any time during the curation and approval period of a screen. In addition, the public access to deposited data can be restricted via a password for a period of up to 2 years.

  2. User Registration

    3. The first step in the upload process is the registration of a new user on the login page. The email address will be used as user name.

  3. Upload Steps

    1. Name-Value Syntax

      2. To provide maximum flexibilty for custom data fields and hyperlinks, ChemMine uses a simple name-value pair syntax to define annotation information. Text with commas or special characters needs to be enclosed by triple-single quotes: '''...'''. Placing the text in a pair of curly brackets allows the creation of sub-categories (bullets). Hyperlinks can be created with the standard HTML tag: <a href="my_URL">my_URL_name</a>

      Example 1: basics 
          Name1 : value1,
    Name2 : value2,
      Result 1 on annotation page:
      • Name1: value1
      • Name2: value2

      Example 2: special characters 
          Name1 : '''cat, dog, mouse''',
      Result 2 on annotation page:
      • Name1: cat, dog, mouse

      Example 3: hyperlinks 
          Name1 : '''<a href="http://www.google.com">Google</a>'''
      Result 3 on annotation page:

    2. Screen Annotations

      1. Name of Screen

        2. Example: 
           Link Between Endomembrane Trafficking and Gravitropism

      2. Description of Screen

        3. Example: 
           To establish a link between endomembrane trafficking and gravitropism, 
   we screened for compounds that affect the gravitropism of    seedlings.
   The full data set of the primary screen was uploaded to identify plant 
   bioactives (e.g. germination inhibitors).
      3. Name of Principal Investigator (PI)

        4. Example: 
           Natasha Raikhel

      4. Access Permissions

        5. Example: 
           Public (or Private)

      5. Annotations of Screen and Biomaterial

        6. Example: 
           Forward Screen : yes,
   Target Pathway: '''intersect between endomembrane trafficking and gravitropism''',
   Gene Ontology : '''Accession: <a href="http://www.godatabase.org/cgi-bin/amigo/go.cgi?view=details& search_constraint=terms&depth=0&query=GO:0009630">GO:0009630</a>, Term: gravitropism, Ontology: biological_process, Definition: The orientation of plant parts under the stimulation of gravity.''',
   Screening Material : {
       Organism : Arabidopsis thaliana,
       Ecotype : Columbia (Col-0),
       Genotype : Columbia (Col-0),
       Tissue and/or Cell Type(s) : '''seedlings''',
       Plant Ontology : '''Accession: <a href="http://www.plantontology.org/amigo/go.cgi?view=details&show_associations=terms&search_constraint=terms&depth=0&query=PO:0000012">PO:0000012</a>, Term: apical hook, Ontology: plant_structure, Definition: Hook-like structure which develops at the apical part of the hypocotyl in dark-grown seedlings in dicots.''',
       Sample Age : 3-5 days,
       Growth Conditions : '''~12 sterilized seeds in each well of 24-well plates 
                              with MS medium were grown in the dark vertically for 48h 
                              and then gravistimulated for 24-72h.'''}
      6. Image to Illustrate Screening Concept

        7. Select in selection menu the option 'upload image file'.
        Example: 
                Title: Concept of Screen
        Description: Screen for chemicals that affect gravitropism. 
        Upload image file: preferred formats jpg, gif or png.

    3. Compound Annotations
      1. Publications

        2. Example: 
                Title: Publication for this compound
        Compound Library: ChemBridge Microformat
        Compound ID: 5263936
        Surpin M, Rojas-Pierce M, Carter C, Hicks GR, Vasquez J, Raikhel NV. (2005)
        The power of chemical genomics to study the link between endomembrane system components and the gravitropic response.
        Proc Natl Acad Sci U S A 102, 4902-4907
        http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15772170
      2. Compound Annotation Sheet

        3. Example: 
                Title: Compounds
        Compound Library: ChemBridge Microformat
        Compound ID: 5263936
        Description: Evidence for Bioactivity
        Extra Annotation:
              Evidence for Activity: visual phenotype,
              Gene Ontology: '''Accession: <a href="http://www.godatabase.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=GO:0009630">GO:0009630</a>, Term: gravitropism, Ontology: biological_process, Definition: The orientation of plant parts under the stimulation of gravity.''',
              Plant Ontology: '''Accession: <a href="http://www.plantontology.org/amigo/go.cgi?view=details&show_associations=terms&search_constraint=terms&depth=0&query=PO:0000012">PO:0000012</a>, Term: apical hook, Ontology: plant_structure, Definition: Hook-like structure which develops at the apical part of the hypocotyl in dark-grown seedlings in dicots.''',
              URL1 : '''<a href="http://bioweb.ucr.edu/scripts/seqview.pl?database=all&accession=At1g06680">At1g06680</a>''', 
              URL2 :'''<a href="http://bioweb.ucr.edu/scripts/seqview.pl?database=all&accession=At1g76450">At1g76450</a>''',
              URL3 :'''<a href="http://bioweb.ucr.edu/scripts/seqview.pl?database=all&accession=At1g77090">At1g77090</a>''',
              IC50: NA,
              LC50: NA

        

                  Assay 1 (required)
                Name: visual phenotype after gravistimulus 
                Description: 12 sterilized seeds in each well of 24-well plates were grown in the dark vertically for 48 and then gravistimulated for 24-72h
                Confidence Score for Bioactivity: 0-5
                        0: not active (applies also to false positives)
                        1: active in primary screen
                        2: active in primary and secondary screen
                        3: active in all previous and follow-up screens
                        4: target protein(s) identified 
                        5: selectivity for target protein(s) demonstrated  
             Tested Concentration Range of Bioactivity: 50-100 uM (25 ug/ml) in 0.5% DMSO
          Assay 2 (optional)
          Assay 3 (optional)
      3. Text file

        4. Example: 
                Title: Mapping table
        Compound Library: ChemBridge Microformat
        Compound ID: 5263936
        Description: CMP-to-image mappings
        Upload text file: for tabular data, please use tab-delimited text files (e.g. exported from Excel)
      4. Image file

        5. Example: 
                Title: Image to illustrate phenotype
        Compound Library: ChemBridge Microformat
        Compound ID: 5263936
        Description: CMP 5263936 maps in image 10626a.jpg to 24-Well1_A02
        Upload image file: preferred formats jpg, gif or png.
      5. Reference Image

        6. Example: 
                Comment: this image will be directly associated with previous image (no CMP ID necessary)
        Upload image file: preferred formats jpg, gif or png.
      6. Upload any other file type

        7. Example: 
                Title: Time course movie
        Compound Library: ChemBridge Microformat
        Compound ID: 5263936
        Description: movie to illustrate phenotype in time course
        Upload any other file: any file type can be used here for download purposes (content not viewable on interface!)
  4. Screening History of Compounds

    5. Users who deposit bioactivity data to ChemMine will be asked to provide a list of all compounds (publicly sharable ones) that were tested in a screen. This allows ChemMine to provide the information about all compounds that were not active in a given assay.

  5. Accessing Screening Data

    6. The bioactivity data in ChemMine can be queried and viewed on two main levels:

    1. Screen Overview Pages

      • Retrieval of all active CMPs of a screen
      • Hyperlinked to compound annotation pages
      • Filtering of compound sets by confidence filters
    2. Compound Annotation Pages

      • Cheminformatics utilities
      • Access data from various screens
      • External links to data from specific CMPs

  6. Editing of Uploaded Information

    7. The screen overview pages have a viewing and editing mode (selectable in upper right corner). When the owner of a screen is logged in then cursing with the mouse over the entries will open a popup menu that allows to edit and delete existing information or to insert new fields (e.g. hyperlinks). The edit mode needs to be used to remove or add entire entries form a screen (e.g. compounds or data files).


  7. Troubleshooting

    8. If you encounter problems with this service, then please email Thomas Girke.


  8. Help Us to Improve this Service

    9. Suggestions to improve this resource can be sent to Thomas Girke.

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