Index

1. Introduction
2. User Registration
3. Upload Steps
1. Name-Value Syntax
2. Screen Annotations
3. Gene Annotations
4. Accessing Screening Data
5. Editing of Uploaded Information
6. Troubleshooting
7. Help Us to Improve this Service

1. Introduction


BAP DB (Bioassay and Phenotype Database) is a versatile Wiki-like content management system (CMS) for diverse bioassay and screening data. External and internal users can upload their data via a web browser. The interactive interface allows the 'owners' to modify, expand and delete their deposited assay data any time. In addition, the public access to deposited data can be restricted via a password for a period of up to 1 year.



Please note: the advanced features of this service can only be used with the web browser Firefox. Alternative browsers, like Safari, Flock, OmniWeb, Seamonkey, Galeon and Epiphany will be compatible with most features in BAP DB. However, Internet Explorer will only allow viewing of the database content, but not uploading and managment of the data. This restriction is necessary because Internet Explorer does not support the latest web standards that are necassary to deliver the best web interface for screening data.
2. User Registration


The first step in the upload process is the registration of a new user on the login page. After the registration, a new account needs to be activated by the database administrator. For this, new users are asked to email an account activation request to Thomas Girke. A short project description should be included in this email.
3. Upload of Screening Data



1. Name-Value Syntax


To provide maximum flexibilty for custom data fields and hyperlinks, BAP DB 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 braces allows the creation of sub-categories (bullets). Hyperlinks can be created with the standard HTML tag:

<a href="my_URL">my_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:
• Name1: Google
2. Screen Annotations
1. Name of Screen


Example:

	 Upload Demo: Hypoxia Screen

2. Description of Screen


Example:

	 The approach is to test mutant plants for resistance or susceptibility to stresses including water deficit, salt, high light, heat, chilling, freezing, anaerobiosis, heavy metal and oxidative stress. The primary goal is to begin a systematic approach to evaluate the contribution of all Arabidopsis genes to stress tolerance. 

3. Name of Principal Investigator (PI)


Example:

         Julia Bailey-Serres

4. Funding Source


Example:

	 NSF-2010 0420152, 0420033
	       or 
	 <a href="http://bioinfo.ucr.edu/projects/internal/Unknowns/external/index.html">NSF-2010 0420152, 0420033</a>

5. Access Permissions


Choose one of these three options:

	 Accessible to all
	 Accessible to registered users
	 Accessible to owner only

6. Annotations of Screen and Biomaterial


Example:

         Type of Screen : growth and development of seedlings under different abiotic stresses,
         Target Pathway: '''stess reponse pathways''',
         Gene Ontology : '''Accession: <a href="http://www.godatabase.org/cgi-bin/amigo/go.cgi?view=details&search_consstraint=terms&depth=0&query=GO:0006950">GO:0006950</a>, Term: response to stress, Ontology: biological_process, Definition: A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).''',
         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:0007131">PO:0007131</a>, Term: seedling growth, Ontology: plant structure, Definition: Growth of embryo after imbibition up to the development of the first adult leaves.''',
             Sample Age : 3-5 days,
             Growth Conditions : '''~12 sterilized seeds in each well of 24-well plates 
                                    with MS medium were grown without stress for 48h 
                                    and then stressed for 24-72h.'''} 

7. Image to Illustrate Screening Concept
Select in the selection menu the option 'upload image file'.



Example:

         Title: Concept of Screen
         Description: Screen for genes that are involved in stress response pathways. 
         Upload image file: preferred formats jpg, gif or png. 

8. Global Reference Image
A 'global reference image' is an image that is used as a reference for many or all phenotype images in a screen. To upload one, select in the selection menu the option 'global reference image'.



Example:

         Title: Global Reference Image
         Description: Reference image for many or all phenotype images. 
         Upload image file: preferred formats jpg, gif or png. 

3. Gene Annotations
4. 1. Publications
   
   
   Example:

            Title: Publication for this gene
            Organism: Arabidopsis thaliana
            Gene ID: At3g10020
            Gollery M, Harper J, Cushman J, Mittler T, Girke T, Zhu JK, Bailey-Serres J, Mittler R (2006)            
            What makes species unique? The contribution of proteins with obscure features.
   	 Genome Biol 7, R57  
   	 http://www.hubmed.org/display.cgi?uids=16859532
   

   2. Gene Annotation Sheet
   
   
   Example:

            Title: Stress responsive gene
            Organism: Arabidopsis thaliana
            Gene ID: At3g10020
            Extra Annotation:
                 Evidence for Gene Function: 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>'''
   

   3. Text file
   
   
   Example:

            Title: Mapping table
            Organism: Arabidopsis thalina 
            Gene ID: At3g10020
            Description: Gene-to-image mappings
            Upload text file: for tabular data, please use tab-delimited text files (e.g. exported from Excel)
   

   4. Image file
   
   
   Example:

            Title: Image to illustrate phenotype
            Organism: Arabidopsis thaliana
   	 Gene ID: At3g10020
            Description: The roots are shorter in the stressed seedling samples.
            Upload image file: preferred formats jpg, gif or png. 
   

   5. Reference Image
   A single reference image can be assigned to another image by uploading it first as standard image file as above. After this, the image-to-reference image association is established in the 'Edit Mode' by clicking the 'View' option next to the image and dragging the camera icon of a reference image into the reference image field. The separate display of a reference image can be disabled by unchecking its viewing check box in the edit mode.
   
   Example:

            Title: Image to illustrate phenotype
            Organism: Arabidopsis thaliana
   	 Gene ID: At3g10020
            Description: The roots are shorter in the stressed seedling samples.
            Upload image file: preferred formats jpg, gif or png. 
   

   6. Upload any other file type
   
   
   Example:

            Title: Time course data in Excel or movie format
            Organism: Arabidopsis thalina
            Gene ID: At3g10020
            Description: Excel or movie to illustrate phenotype in time course
            Upload any other file: any file type can be used here for download purposes.
   

4. Accessing Screening Data


The bioassay and phenotype data in BAP DB can be queried and viewed in two ways:
1. Browsing through screen list
2. Gene ID search
3. Full-text search
5. Editing of Uploaded Information


The screen overview pages have a viewing and editing mode (selectable in upper right corner). When the owner of a screen is logged into the system, 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. gene annotations or data files).




6. Troubleshooting


If you encounter problems with this service, then please email Eddie Cao or Thomas Girke.




7. Help Us to Improve this Service


Suggestions to improve this resource can be sent to Eddie Cao or Thomas Girke.