Submit a 2D gel on the web to the
2DWG Meta-Database Catalog

http://www-lecb.ncifcrf.gov/2dwgDB/2dwgSubmitData.html

Table Of Contents

1. Introduction

The 2DWG meta-database catalog contains some of the 2D gel images found on the web. A meta-database contains information about data in other databases. We will be refering to this catalog as the "2DWG". Data for the 2DWG is acquired by a conbination of review of results from web searching as well as reviewing submissions by web database authors. The table is organized as a spreadsheet with column headings at the top. Each row corresponds to a gel image with the fields in the row describing the gel. The fields are defined in the Glossary of fields. The rows are sorted by tissue type (the first column field).

In addition, we are soliciting contributions from the 2D gel Web server community. This data entry form can be used for submitting a new entry to the Editor of the 2DWG database for review and inclusion.

1.1 Criteria for data to be submitted to 2DWG

Note that the data you will submit describes a 2D gel image residing on your web server. Your web server should have supporting information reguarding that gel. This should include:
  1. Gel images. (If you are using pseudo-images, we suggest also supplying raw, i.e. stained or autorad, images, which are easier to compare with gel images from other labs.)
  2. Protocol for running the gel (including apparatus, detection method, CA or NEPHGE or other, IEF or IPG or other, pH range, Mr range, etc.)
  3. Protocol for sample preparation
  4. Image map identifying proteins. (This can be a static labeled map or a dynamic map where one could click on a spot to cause that web server to report the information on the corresponding protein identification.)
  5. References to the refereed literature where the biomedical data and protocols are described
  6. Other information useful for interpreting the data should also be included

Remember, it much more convenient for readers to have access to this information on-line in your server through hypertext links since it may be difficult to get journal papers, tech-reports or books which are not widely available. Not all libraries can afford to subscribe to all journals.

Gel images themselves are not submitted to 2DWG, only information about them. This is because 2DWG is a meta-database that describes data residing on other web or FTP servers. The image files are generally in GIF, JPEG or TIFF file formats which are suitable for Web browsers. Web addresses or URLs (Universal Resource Locators) are used to define links to these other web databases. They may only use the "http://" or "ftp://" protocols. Image size should be 8-bit grayscale or color and approximatey 500 to 1000 pixels (in both dimensions). Since the data is to be used for viewing - not quantitation, very high resolution is not needed.

1.2 Electronic peer review by referees over the Web

We are in the process of implementing an electronic peer review of submitted materials by 2DWG Editorial Board members. When data is submitted, it will be E-mailed to these reviewers who will respond within a short time. The reviewers will interact with a 2DWG staging server (different from the 2DWG) where they can judge the material. Materials of sufficient quality will be included in the 2DWG. We plan to implement an "Accept/Reject/Revise with comments" system with submitter notification by E-mail. As this submission and review process is experimental, we forsee changes being made as we gain experience.

Some of the reviewer criteria (some of which was suggested by the ExPASy group) will be:

  1. Content is relevant and of academic value
  2. Correctness and completeness
  3. Quality and Clarity
  4. Contains valid and relevant links - especially maps and related information
The Editor will periodically review the data and mark entries which are no longer available (i.e. not simply because their server is down one day).

There are a number of ways that Laboratories which want to publish 2D gel databases on their web server can do so. The current version of the HTML 3.2 language supports client-side image maps (see any referece on HTML 3.2). Many of the commonly available Web editing programs will let you do easily setup these maps. Other more advanced methods are available including: a simple database search engine dbEngine which creates a searchable database on web server; the ExPASy group will be offering 2D gel web publishing software as well.

1.3 Procedure for submitting data using forms

First fill out the information on who you are. This information will NOT be put into the public database. It is used only when we have to get in touch with you to clarify information about the data.

Second fill out the information about your gel entry. We suggest you review other data in the 2DWG to see the typical responses you might use. Fields which must be filled in are indicated in magenta, otherwise the field is optional. Optional fields in the table with no data will be indicated with a '-'.

Third, click on Submit Data below to send the filled in form to the 2DWG Editor who will review it and then add it to the database.

1.4 How to handle submission errors - correct and resubmit

When you submit the completed form, you may get an error message back that some field or fields is incomplete or incorrect. It will give you a list of exactly which fields are incorrect and may suggest what you may need to do to correct them. Here is what you then do to easily make corrections. First, click on the Back button on your web browser - DO THIS ONLY ONCE OR YOU WILL LOSE WHAT YOU TYPED!!! If you do click more than once, click on Forward to get you back to the page which has the material that you did enter. This will bring you back one level in the browser to your form with your entries intact - just as you typed them. Then, change just those fields which were incorrect and then finally submit the form again. If you make the corrections this way, you do not have to retype all of the fields in the form just to correct a few errors.

If the submission process to the Editor has been successful, an accession number will be assigned and reported back to you in the confirmation. The accession numbers are of the form "WGnnnnn" where nnnnn is a sequential number. If you want to make corrections in the future regarding this entry, send email to the Editor describing the changes indicating the "WGnnnnn" identifier.

1.5 How to enter multiple gels

When you submit multiple gels, there is a simple trick you can use to avoid having to retype all of the fields which are the same. Simple click on the Back button on your web browser (as you did in 1.4 above) until you see the filled in form. Again if you went too far, click on Forward until you get to the filled in form. Then go to the specific fields you need to change and change only those fields. Verify that all of the fields are correct and the just submit it again.

2. Data entry form

2.1 Enter data about your organization

Your Name:

Organization:

(Opt.) Address:

E-mail:

(Opt.) Phone-Nbr:

(Opt.) FAX-Nbr:

2.2 Enter data about your 2D protein gel to be submitted

Tissue or Organelle, definition
(eg. Plasma, Breast, Ecoli, Yeast, Ribosome, etc.)

Species, definition
(eg. Human, Mouse, Rat, Fungi, etc.)

(Opt.) Cell line, definition

Image URL, definition
(I.e. enter the URL of the image on your Web server. See the suggested naming convention for 2D gel image files offered on the Web. Eg. "http://www.expasy.ch/ch2dgifs/PLASMA_HUMAN/PLASMA_HUMAN.gif". GIF files are preferred. If the image is to be used with Flicker, then the size should be about 500 to 1000 pixels (rows or columns). It is also suggested that the pI orientation be acid to basic (left to right) - although Flicker can flip images horizontally or vertically. )

DB URL, definition
(I.e. the URL for the gel specific database part of the web server. Eg. "http://www.expasy.ch/ch2d/ch2d-top.html")

Isotope / stain / Ab, definition
(I.e. isotope implies autoradiographs or phosphor-imaging (in which case the radioisotope is mentioned); stain (eg. Coomassie Blue or silver for silver stain); and Ab is antibody (eg. anti-PY, anti-p53, etc.)

CA/IPG, definition
(I.e. Carrier-Ampholytes, Immobilized pH Gradient)
CA, IPG

IEF/NEPHGE, definition
IEF, NEPHGE

(Opt.) pH range, definition
(I.e. pH numeric range as 4-8 (acid to basic) or 8-4 (basic to acid)

(Opt.) Mr (Kd) range, definition
(I.e. molecular mass range as 10-200, if molecular weight markers add "mwm")

Lab/Org/Comp URL, definition
(I.e. Laboratory/Organization/Company and top level URL for 2D gel database. Eg. "http://www.expasy.ch/")

Scan/synth/diagrm, definition
(I.e. gel image is Scanned, synthesized or a diagram)
scanned, synthesized, diagram

Map/raw data, definition
(I.e. image is a map or raw data. Or, if a dynamic or static map URL exists, then specify the URL. Eg. "http://www.expasy.ch/cgi-bin/map2/def?PLASMA")
Is a map, Raw image,
Map URL:

(Opt.) Miscellaneous, definition
(Note: up to 160 characters. Hint: you might put a few keywords here to help with searching the 2DWG - especially if the name of the tissue or cell line is an abreviation.)

2.3 Press "Submit data" to send it to the 2DWG Editor for review

to 2DWG Editor for review and adding to the database.

Upon submission, you will get a reply indicating what the table row looks like. The fields with URL link will be active so you can try out the links yourself. If there are any errors in the data sent or future changes or revisions to this entry, please notify the Editor through E-mail at lemkin@ncifcrf.gov - making sure you mention the @DWG WGnnnnn identification number returned in your reply. Note, you can same this confirmation on your computer through your web browser (eg. use the SAVE AS option in the FILE pull down menu in Netscape).

this will clear all entries - ARE YOUR SURE you want to do this?

$Date: 1999/07/19 14:54:15 $ / The 2DWG database editor-in-chief is P. Lemkin. Send comments and suggestions to lemkin@ncifcrf.gov
The 2DWG resides on the LECB, NCI/FCRDC web server.