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Background :
 
 
Funded by the

Streptomyces coelicolor 2D Gel Protein Database

Overview

General

This site allows a user to navigate 2D image gels, and view the details of various known spots. If the user is authenticated they are able to identify new spots, add proteins to the system and create groups of proteins.

One of the self imposed requirements for the site was that there is a link between the user who entered the data and the data itself. Therefore it is possible to see who submitted, for example, a protein along with when. The database also holds records of when a record was last updated and by who.

Initially, the system was designed to allow for ownership of data, where for example, only the user who entered the data could update it, however it was thought that this might create too much inflexibility. Therefore there are no restrictions over what one authorised user can do to anothers data. It is left to the user to show consideration when deleting information - of course if something is deleted by accident please contact the webmaster and ask for the record you deleted to be restored from a backup of the database (for this to be successful please provide as much information as possible about the record, e.g. a protein's ScoDB number, or for a spot the gel it was on and what protein it was associated with (and if possible the coordinates).

If errors occur while you are attempting to undertake operations, or if something goes wrong, you should be displayed error messages in Red which should hopefully give you some idea of what has gone wrong. Not all error messages are fatal.

If you are an authenticated user, to identify spots on an image gel, you will need to firstly add a protein to the system (or use an existing protein, if it is applicable). One protein can have multiple spots on many different images.


Login

Logging in will give you as a user the ability to :

  • add proteins,
  • add proteins to groups,
  • create groups,
  • identify spots on images

If you already know your username and password then proceed to this page and fill in the boxes. If you do not have a login then please email the webmaster (g.velarde@umist.ac.uk) who will set up an account for you. It is likely that account ownership may be limited to certain predefined users, unless you have a good case for having one (e.g. you have experimental data you wish to store).

Users who are not able to login, will only be able to view the data held in the database. This will hopefully lead to high quality data being held in the system

Proteins

Adding a Protein into the database

Before you can identify a spot on an image, you need to have already entered the relevant protein into the system. To do this, you must know the Sco (Streptomyces coelicolor) database number (in the form of SCONNNNN, where M is 0-9), as well as the Protein Classification (a drop down list is given for this, based upon the modified Riley index.

For more information on the Sco database please visit here (this is another BBSRC funded project)

All other details are optional, but should be entered if possible.

To add a protein go here.

Viewing a protein's details

The protein details page is perhaps the most useful to users of this site. It provides users with details of the protein itself (for example the protein's classification, whether there is any structural data on the protein (SuperFamily) along with links to other databases (NCBI, SWICZ and the ScoDB.). Becase this page makes external connections to other pages to bring in external data (e.g. the SuperFamily data) it is unfortunately one of the slowest pages to load, however it is hoped that the benefits of having a lot of information in one place will offset this.).

The fields in the main "Protein Details" table are as follows :

  • ScoDB Reference - this is the reference the protein has been given from the Streptomyces coelicolor database (ScoDB) (another BBSRC project). Every protein in this database must have a ScoDB number. The ScoDB Reference takes the form of SCO followed by any 4 digits (0000 to 9999).
  • Other Gene Designations - these are other designations available for the same protein, possibly including ORF numbers.
  • Gene Product - this field is normally populated by data taken from the ScoDB.
  • Protein MW - this is the molecular weight of the protein measured in Daltons (Da). Please note that this is a theoretical value taken from the ScoDB (normally) although it may have been altered by a curator
  • Protein pI - this is a measure of the pH of the protein. Again this is a value which is taken from a theoretical value supplied by the ScoDB when the protein was added
  • Protein Classification - this uses the modified Riley index which can be found online here. The Riley index is based upon work undertaken by Monica Riley and collegues for E. coli (ecocyc.org) and has been modified for S. coelicolor.
  • Added to DB By - this tells you who added this protein to the database. It is purely for informational purposes.
  • Added to DB On - this tells you when the protein was added to the database.
  • Last updated by - this tells you who updated this protein last.
  • Last updated on - this tells you when the protein's entry in this database was last updated.
  • Other details/notes - this is a free text area which is capable of displaying any additional information related to the protein which is not covered by the above fields, but someone has felt is required.

After the details mentioned above, authorised users are presented with buttons to edit or delete the protein, and also a button allowing them to add this particular protein to an existing group (See here

Links to other databases - Next users are shown links for thie protein in external databases. Currently three databases are supported, namely :

  • SWICZ - search for proteins identified there with a similar pI and MW. Unfortunately SWICZ doesn't seem to detail ScoDB numbers, so a direct search is not yet possible, although it could be implemented in the future using the "Other Designations" field mentioned above.
  • ScoDB - this links directly to a protein with the same ScoDB Number. The ScoDB allows the user to view the Cosmid details, along with other information
  • NCBI - this provides further details about the protein. It is linked by the ScoDB number.

Next if there is any Super Family information available for this protein it is displayed here. Please note that this information is not held locally in this database, and is instead retreived from the BBSRC each time (this is one reason why the protein details page is so slow to load!). It was felt that providing information on structural information would be of use to researchers (and saving you having to follow a link or two to find it!) so it has been included in this page. Because the information is not stored locally it is not possible to search by any of the Super Family data.

Next you will see the groups protein belongs to, if the protein belongs to no groups then none will be displayed, otherwise they will be listed. Clicking on one of the links will take you to a "Protein Group Details" type page where the details of the group are displayed along with all other proteins which belong to the group. See the help section on protein group details for more information.

Finally you are shown which Spots are associated with the protein. Clicking on one of the links will take you to a page which displays the details of that particular spot (see the help section for Spot Details for more information).

Deleting a protein

To delete a spot from the database, you firstly need to have logged in (see here).

After logging in, when viewing a protein's details (here) or from the Proteins page you will have the option of deleting a protein. Before deleting the protein the system will ask you to confirm that you have selected the right protein, and will warn you if there are any identified spots associated with the protein (deleting the protein will result in any identified spots being deleted as well).

Updating a protein

To update a protein, you firstly need to have logged in (see here).

Once you are logged in, if you either go to view the specific protein's details (see here) or go to the Proteins page, from which you will be presented with a list of options available, one of which will be to &Quot;Edit and existing protein" . After selecting the appropriate protein from the drop down box, and then clicking Go you will be taken to form which has blank spaces for you to fill in details.

For a description of the fields displayed please see here.

If you click on the "Synchronise with ScoDB" button, some of the fields will be automatically updated with values which are contained within the Sco Database (pI, mw, Gene designations, and Gene product).

Once you are happy with the changes you have made to the protein, click on the submit button, and the database will be updated. If there happen to be any errors these will occur in red text.

Image Spots

Image spots

A spot in this system represents part of a reference gel which has been identified as being produced from a certain protein. Identified spots are marked on the reference gels with '+' signs. To navigate the reference gels, please click here where you will be shown a list of available gels in the system.

How to identify a spot / Link a spot to a known protein

To enter into the database a newly identified spot

  1. Log into the website
  2. Browse to where the spot is on the reference gel, starting from the View Gels page. (For help on navigating the reference gels click here)
  3. On locating the unidentified spot, click on the "Add new entry" button (below the larger image on the web page).
  4. After clicking on the &Quot;Add new entry" button, you will be presented with a page asking you to click where on the portion of the gel you wish to place the marker for the spot. Click on the appropriate place on the gel.
  5. If you find that you have positioned the spot in the wrong place, click on the "Go Back" button which will allow you to choose where to put the marker again.
  6. Next you will be asked to select a protein to associate with the gel, and for the MALDI-ToF data along with any notes you might have which are of relevance.
  7. Once the form is filled in, click &Quot;Submit" and it should all be completed for you

Viewing the details of a spot

To view the details of a spot, click on the "View Gels" button in the menu on the left hand side, select which image you are interested in, and use the navigation tool to find the appropriate spot. Once you have the spot displayed in the left hand "zoomed in" picture, you will be able to click on it to reveal further details. A description of the fields is given below.

Alternatively, you can find the appropriate spot from the "Search" page, or from a listing in the "Protein Details" page in the "Identified Spots associated with this Protein".

The spot details page contains the following details :

  • ScoDB Reference - this is a hyperlink to the appropriate details of the protein which this spot is associated with.
  • MALDI-ToF - this is data gathered from a mass spectrometer, and can be used to measure the degree of confidence that this spot does indeed belong to a particular protein. The "Protein Coverage", "Matched Peptides" and "Mowse Score" fields all form the MALDI-ToF data.
  • Image Name - this lets you know what image the spot is located on. The hyperlink will display the details of the particular image
  • X Coordinate - this is the X pixel value on the raw image where the spot is located. It is really an arbitary measurement, and should only be used to differentiate between spots on the same image.
  • Y Coordinate - this is the Y pixel vale on the raw image gel where the spot is located. The same points apply to this as to the X Coordinate value (see above).
  • Added by - this identifies the person who identified the spot and entered the data in the table.
  • Added on - this tells you when the entry in the database was added.
  • Notes - this contains any notes on the spot itself, for example experimental observations or other non-normal events which might be of interest to the user.

After the table showing the details of an identified spot, the user is able to view the spot on an image gel by clicking on the "View on Gel" button.

Users who have logged in will also be presented with buttons to Edit or Delete the spot

Deleting a Spot

To delete a spot from the database is only possible if you are logged in.

Once logged in you can either use the Search page or browse to the spot on one of the reference gels. Once you find the spot you require, you can go to view it's details, from which a button will be visible allowing you to delete or update it. Clicking on the delete button will result in you being asked to confirm that it is the spot you wish to delete. Clicking Delete again will result in the spot entry being removed from the protein gel.

Updating a spot's details

If you go to view the details of a spot (see here) when logged in you will be presented with an update button, which will take you to a screen where you can alter the details of a spot (e.g. the protein which is associated with it, or the MALDI-ToF information).

Protein Group

This site gives authorised users the ability to create arbitary groupings of proteins which may interest them. Any user is able to filter the identified spots they are shown in on one of the reference gels by Protein Group - for instance they may only wish to see spots belonging to a particular Protein Group. A Protein Group can compromise of one or more proteins. If it is empty the user should only be able to add proteins to it.

Adding a Protein Group

Protein groups can be thought of as an arbitary grouping of proteins, which can be created by any authorised user. Currently protein groups can only be used in searching, but they should soon be visible in the image gels as well. To add a protein group go here and to add proteins to a protein group go here

Viewing the details of a Protein Group

To view the details of a protein group go to the Groups page and select from the drop down list which group you would like to view the details for

Removing a Protein from a group

If you wish to delete a protein group, then go here. Assuming you are logged in you will be able to select the "Delete a Group" option. You will be prompted if there are proteins in the group (just incase you've picked the wrong group), and will be asked to confirm if it is the group you wish to delete.

You can delete groups if there are proteins registered within the group, the proteins will afterwards no longer belong to that group (as it no longer exists).

Protein Grouping

This is where the user adds particular proteins to a group, in order to filter the spots which are visible upon the reference gels.

Adding a Protein to a Protein Group

Proteins can be added to any Protein Group.

There is no limit to how many proteins you can add to a particular group. To add a protein to a group please go here and select the appropriate option (requires that you are logged in)

How to Remove a Protein from a group

Proteins can be removed from a group using the "Remove a protein from a group" option from Protein Grouping page. Upon selecting which group you wish to remove a protein from, you will be asked to select the protein, and then confirm that you have chosen the right protein before it is actually deleted.

Deleting a protein from a group does not delete the protein entry itself, so don't worry!

Identifying a spot on a gel

To identify a spot on an image gel, you need to go here and select which image you wish to use. You can then click on the smaller right hand side image (Which can be thought of as being a navigation device) which dictates what is visible in the left hand image. On looking at the right hand image you will notice there is a yellow box in the image, around the point where you last clicked. This yellow box will move to where ever the user clicks, and marks out the area which is shown in the image on the right.

When you search to the appropriate place, and find the spot you wish to identify, click on the "Add New Entry" button. This will now allow you to select the spot you wish to view on the image on the left, clicking on the spot once will result in a green spot appearing on the image where you clicked. You will now be prompted for details for the gel, select the appropriate protein from the drop down box, and fill in the other details if you can.


Searching the database

If you wish search through the database you can go to this page here which contains various methods of searching through the database. Should any further methods be required, please contact the webmaster, and if possible they will be added

Current options available to the user to use when searching the database are :

  • Protein Related
    • Find all proteins with classification - after selecting which classification, will show the user all proteins that belong to the classification. There may be between zero and many matchs
    • View Proteins in group - this will show the user which proteins are in a particular group. (see here for more information on Protein Groups.)
    • View Proteins with a designation containing - this allows the user to enter a particular string and search for it - e.g. entering "Foo" would search for all proteins which contain "Foo" in their designation. The search is not case sensitive.
    • View Proteins with a Gene product containing - this is similar to the previous entry, although it searches for proteins with a gene product matching the field the user enters.
    • View proteins with a pI between - this allows the user to view all proteins which have a pI between the values selected by the user (range from 1 to 14).
    • View proteins with a mW between - this allows the user to search between two molecular weights (in Daltons). Any proteins which fall within the range will be displayed.
    • Find all proteins submitted by - this allows the user to view the proteins which a particular user has entered into the database.
    • View proteins by Image - this allows the user to view all proteins which have been registered with a particular image
    • Find a particular protein by SCO Number - this allows the user to view the details of a particular protein (selected from a drop down list)
    • View all proteins ordered by - the allows the user to view the all proteins ordered by one of :
      • Added By
      • Added On (Most Recent First)
      • Added On (Oldest First)
      • Updated On (Most Recent First)
      • Updated On (Oldest First)
      • By pI (Ascending)
      • By pI (Descending)
      • By MW (Daltons) (Ascending)
      • By MW (Daltons) (Descending)
  • Gel Related
    • View Spots Identified by - this allows the user to view all spots identified by a particular person. This might be of interest if you know a particular person is working on a similar thing to what you are
    • View Spots associated with protein - this allows you to view all spots which are associated with a particular protein - so if you wanted to find all identified spots for your favourite protein, this is the option for you
    • View all spots on an image - this allows you to view all spots which are on a particular image (so saving you having to visually browse an image).
    • View spots with protein coverage between ... - this allows you to search by the MALDI-ToF mass spectrometer reading for the protein coverage
    • View spots with a Mowse score between ... - this is another MALDI-ToF search, this time for the Mowse score
    • View spots with matched peptides between ... - this is the final MALDI-ToF search, this one is for the Matched Peptides field.
  • Image Related
    • View Details of a gel - this allows you to view the details of a particular gel. You can also use this as a starting point to browse a gel from.
    • View Proteins identified on a gel - this allows you to view all proteins which have been identified on a particular gel, just select which gel you are interested in and click 'Go'
  • User Related
    • View Details of a particular user - this allows you to view the details of a particular user.

Linking to this database from other projects

In order to make this application useful for the community, it is possible to link to it from other websites directly, so providing the end user with a more integrated experience. Methods available, are listed below.

External Script

This has been designed to allow an external site to connect to a script (Available at here as an example). The output of the script is unformatted text, which should be easily parsable by another script, so allowing output from the database running this site to be appended into a webpage on a remote site. Output from this script would look like the following : 

SCONumber: SCO0247
AddedBy: David Goodwin
AddedOn: 2003-02-14
MALDI-TOF/MowseScore: 45
MALDI-TOF/MatchedPeptides: 456
MALDI-TOF/ProteinCoverage: 10
ImageURL: http://qbab.aber.ac.uk/s_coeli/new-gel//imageView.php?imageName=The original
reference gel
SCOURL: http://qbab.aber.ac.uk/s_coeli/new-gel//proteinDetails.php?proteinId=SCO0247
-END OF RECORD

If there happen to be more than one spot associated with a particular protein then all results will be displayed, in a format similar to :

SCONumber: SCO0247
AddedBy: David Goodwin
AddedOn: 2003-02-14
MALDI-TOF/MowseScore: 45
MALDI-TOF/MatchedPeptides: 456
MALDI-TOF/ProteinCoverage: 10
ImageURL: http://qbab.aber.ac.uk/s_coeli/new-gel//imageView.php?imageName=The original
reference gel
SCOURL: http://qbab.aber.ac.uk/s_coeli/new-gel//proteinDetails.php?proteinId=SCO0247
-END OF RECORD
SCONumber: SCO0247
AddedBy: David Goodwin
AddedOn: 2003-02-14
MALDI-TOF/MowseScore: 12
MALDI-TOF/MatchedPeptides: 123
MALDI-TOF/ProteinCoverage: 45
ImageURL: http://qbab.aber.ac.uk/s_coeli/new-gel//imageView.php?imageName=The original
reference gel
SCOURL: http://qbab.aber.ac.uk/s_coeli/new-gel//proteinDetails.php?proteinId=SCO0247
-END OF RECORD

The above has been designed to be easily machine readable. If any other search functions are required then it should be relatively easy to add them.

Viewing a Proteins details

If you wish to view a protein's details directly then create a link to the proteinDetails.php page with a url similar to proteinDetails.php?proteinId=SCO0247

.

Other ways...

Depending upon what the external site already knows it is possible for many other links to this site to be made, by either posting directly to this site, or using get requests. The particulars of this are visible for all to see (in the html source code). A good place to start would be the search / searchResults PHP files.