Operating Guidelines and Conditions of Use for Editors of the DOD

All information held in the DOD is classified into "Branches" and "Columns", and presented hierarchically in descending order according to specificity. Information is added by "Objects" which are vehicles for ICs and "Content Items", e.g. the specific journal article:

Chatenoud L, Bach JF. Questioning Four Preconceived Ideas on Immunotherapy of Clinical Type 1 Diabetes: Lessons from Recent CD3 Antibody Trials. Rev Diabetic Stud 2005. 2(3):116-120.

is an object of the IC "Journal Articles" and, simultaneously, a Content Item of the Column "Anti-CD3 Therapy" within the Branch "Diabetes OD > Reversal/Prevention of Diabetes > T1DM > Re-establishing Tolerance > Modifying Immunity > Recent Onset > Systemic Intervention > T cells > Anti-CD3 Therapy". Thus, any Column within a Branch of the DOD may contain Content Items that are Objects of different ICs. Terms of the DOD nomenclature are summarized in Table 1.

**Table 1.** DOD nomenclature
	Content-related	System-related
Low specificity	Branch	Information Category
Moderate specificity	Column	-
High specificity	Content Item	Object

General permissions of Editors and users

At first, users and Editors are required to log in in order to add or change Content Items. Editors are allowed to add Objects of any IC to their Columns. This is different from the permissions regular Individual or Institutional Users have. Individual Users can add only Discussion Articles, Comments, Discussions, Conference Announcements, Job Applications and Information/News (they cannot add Journal Articles, Availabilities or Grants/Funds). Institutional Users can add Journal Articles (but only through file upload), Conference Announcements, Availabilities and Grants/Funds (they cannot add Discussion Articles, Comments, Discussions, Job Applications or Information/News).

Each user is able to add Content Items anywhere in the directory and edit Content Items he or she has already submitted. However, users cannot move Content Items or change Content Items they have not submitted themselves. Editors have extended access authorization: they are allowed to change and move any Content Items included in the Columns they supervise. An Editor may also move a Content Item into another Column not assigned to him/her.

When an Editor logs in through the regular log-in menu on DOD, links appear for each Column assigned to that Editor below the "Account" section at the left-hand navigation menu. These links are always present as long as the Editor is logged in independently of his location within the DOD. The Editor can access his/her Columns directly by clicking on these links. Content Items cannot be moved directly within the DOD but only within a kind of interface, the ZMI (Zope-based Content Management for Science Interface). When Editors are logged in and have accessed a Column they supervise, a further section appears below the Account section within the left-hand navigation menu, titled "Administration". Within this section the "Directory" link leads to the ZMI or, more precisely, to the Branch or Column to which the Editor is assigned. Editors can access only those locations within the ZMI which are assigned to them. Please refer to the respective section below to learn how to work with the ZMI.

Finally, Editors are permitted to add new Columns below the Columns they supervise. This is a crucial procedure, since Content Items must always be added to the most specific and suitable Column. Columns can be added, and added Columns can in turn be changed and moved. These procedures are possible within the ZMI.

Responsibilities of DOD Editors

Each Editor is responsible to edit, control and keep "clean" the content of the Branches or Columns to which he/she is assigned. Responsibilities are divided into mandatory obligations and suggested requirements.

Mandatory obligations are important to maintain the high quality of the DOD, both regarding content and system. Mandatory obligations are:

to add only content to a column which is suitable to that column (this includes the requirement that content is always added to the most specific Column; Editors should enhance the specificity of their Columns by adding new sub-Columns for sub-topics; new Columns are added in the ZMI),
to add information carefully and in accordance with the manual, which explains how the different Objects are to be added (this ensures that the technical quality of the DOD is maintained; therefore, information added must be inherently correct as well as inserted correctly into the set forms),
to correct Content Items that contain striking errors,
to move Content Items that are not suitable for their Columns into other Columns,
to delete Content Items that include content which is not suitable for the DOD at all or which contravenes against law or morality.

Suggested requirements are important for the content-related set-up, development and enhancement of the DOD and, consequently, for its recognition and reputation. Suggested requirements are:

to collect information regarding any IC (e.g. Journal Articles or Grant and Job Offers or a Conference Announcement that is not yet existent in the DOD) and to add this information to the most suitable Column of the DOD, even if this Column is not supervised by the Editor (if the edited Column is not highly suitable and if this Column is supervised by the Editor, the Editor is requested to add new subordinate Columns (with increasing specificity) until there is a Column that is absolutely suitable),
to supervise and coach Discussions opened within a Column assigned to the Editor (this includes replying to questions raised in such Discussions or starting new discussions on own initiative).

In particular, the Editor is requested to add Content Items via Objects of the following ICs to his/her Columns:

Journal Articles highly relevant to the field assigned to the Editor (it is very important that all bibliographic elements, such as the correct abbreviation title of the journal or the format of the references, are inserted correctly in order to ensure proper working of DOD-inherent link functions).
Discussion Articles that are suitable to the Column assigned to the Editor (it is important that the author(s) of the Discussion Articles added to the DOD agree to the publication of their article on DOD; either the addresser/submitter is the author himself or the written consent of the author(s) must be available. The Editor can also publish his/her own Discussion Articles on DOD).
(Own) Comments on Journal or Discussion Articles (note that the corresponding author of the commented article will be notified of any Comments on his/her article).
Announcements of topic-related events, such as conferences, meetings etc.
Offers for job vacancies, grants and funds that are announced elsewhere (it is important that these offers contain the time periods in which they are available).

Application for DOD Editorship

Any user registered as an Individual User can apply for Editorship via the application form available online at http://www.diabetes-od.org/directory/content/editor. As the DOD is owned, maintained and conducted by the SBDR, decisions concerning applications rest with the Executive Board and the Advisory Board of the SBDR. Typically, after receipt of the application the applicant is asked about his/her willingness to contribute to the DOD and to edit it carefully, as well as about his/her field of competence and the desired Columns to be advised. The SBDR representatives make the final decision on the field that the Editor will supervise and a DOD Administrator sets up the authorizations and assigns the Columns to the new Editor.

Remuneration and fees

The Editor will not be paid by the SBDR or any other participating organization. There is neither a remuneration to the Editor nor must the Editor pay any fee.

Acceptance of agreements

There is no written contract between the owner of the DOD (the SBDR) and the Editor. However, with accepting Editorship, the Editor confirms that he is aware about and accepts the conditions of use outlined in this document. In particular, the Editor accepts to being responsible in the way outlined above (in section "Responsibilities of DOD Editors"). Any breach of this agreement will lead to exclusion from Editorship. Should the impression of damage to or confusion in the DOD become apparent, either willfully or through gross neglect on the part of the Editor, the costs for reconstruction can be imposed on the Editor.

Adding and editing of Journal Articles

Before a new Content Item of any kind of IC is added the most suitable Column within the advised field must be identified. If the Content Item is generally suitable for the advised field (or Column) but the existing Columns are of limited suitability, the Editor should create a new Column or, if necessary, a new Branch below the Column he/she advises. After creating the most suitable Column, the Content Item can be added to that Column by the Editor.

Adding of a Journal Article

Editors can add Journal Articles only to those Columns to which they have been assigned editorial permission. To add a Journal Article access the Column that is most suitable. From the menu at the bottom of the page, select "Add a Journal Article" and click on "Proceed". Insert the information as completely as possible. Note the format requirements of the following (selected) fields, other fields are self-explanatory:

First Author's Name: last name (of the first author mentioned in the author list of a Journal Article), space, initials first names, e.g. "Bach JF" (without quotation marks).
Affiliation: insert only one affiliation, typically the one of the first author. No dot at the end of the affiliation.
Other Authors: same format as First Author’s Name. Names separated by commas, e.g. "Godeau F, Chatenoud L" (without quotation mark).
Published in: insert the journal’s abbreviation title according to the NLM abbreviation system, e.g. "Rev Diabetic Stud" (without quotation marks) for "The Review of Diabetic Studies" or "J Immunol" for "Journal of Immunology".
Abstract: insert the full abstract in the text field.
References: important format requirement! Use the text field to insert exactly one reference per line. There must not be any line break within one reference citation. To maintain the correct format for references, the following instructions must be followed:

1. Make sure that each reference has the correct format. Exact adherence to this format is vital, as it is used by DOD mechanisms to calculate cited-in references. The format must be exactly typed as outlined in the following examples (including specific order of bibliographic elements, specific punctuation and spacing):

1. Chatenoud L, Bach JF. Questioning Four Preconceived Ideas on Immunotherapy of Clinical Type 1 Diabetes: Lessons from Recent CD3 Antibody Trials. Rev Diabetic Stud 2005. 2(3):116-120.
2. Martin DA, Zheng L, Siegel RM, Huang B, Fisher GH, Wang J, Jackson CE, Puck JM, Dale J, Straus SE, Peter ME, Krammer PH, Fesik S, Lenardo MJ. Defective CD95/APO-1/Fas signal complex formation in the human autoimmune lymphoproliferative syndrome, type Ia. Proc Natl Acad Sci U S A 1999. 96(8):4552-4557.

2. Open the Windows Editor program (start -> all programs -> tools -> editor). This is a simple text editor.
3. Copy and paste the reference list into the text editor. Please note again, only one line per single reference AND adherence to reference format, as described above!
4. References must be numbered by Arabic numerals followed by a dot and a space, such as outlined in the example above.
5. If there is a long space between the Arabic number and the text of the reference, replace this by a normal space. To do this (i) mark the long space, (ii) click on "Edit" in the task menu of the program and select "Replace", (iii) insert the copied long space into the "Search for" field and insert a normal space into the field "Replace with", (iv) select "Replace all". Then all long spaces will automatically be replaced by normal spaces.
6. Select all. To do this, again click on "Edit" in the task menu of the editor program and select "Select all".
7. Copy this marked reference list into the text field of the respective DOD set form called References.

WWW addresses, HTML links: insert the full-text HTML www link into the field. If possible, make sure that this is the actual full-text link, not the link to the abstract. Sometimes full-text links are "hidden". This is the case if the publishers use restricted site access to full-text pages, such as Elsevier, Springer etc. In this case, you must obtain the full-text link by the following procedure: (i) go to the original publisher site where the abstract of the article is presented, (ii) place the mouse on the full-text link (without clicking), (iii) click with the right mouse button, (iv) select "Properties" from the menu so that you can see the full link, (v) copy the complete link from the properties menu and paste it into the field of the respective text form called "References". Make sure that the complete link is copied and pasted into the field of the text form. Finally, activate the box "Do not valid URLs".
WWW addresses, PDF link: follow the same procedure as for the HTML link.

Once all fields have been filled in press the "Send" button.

Import of references

After a Journal Article including references has been added to the DOD, the references must be imported separately into the DOD, so that they become Content Items. To this end, the DOD has a special import function for references of Journal Articles, called "Import References". To apply the import function, (i) make sure that you are logged in, (ii) access the page that contains the details of the Journal Article for which the references should be imported (stay in the DOD area, do not enter the edit area), (iii) scroll down to the end of the page, (iv) apply the link "Import References". Then a new set form opens where all the bibliographic elements, including author names, (one) affiliation, abbreviation title of the journal, abstract etc., of the first reference article can be entered. When applying the import function, two important issues should be considered:

Firstly, insert the data in exactly the same format as is required for Journal Articles (see above). This means, author names must have the following format: last name, space, initials, first names without dots or spaces, e.g. Bach JF, Chatenoud L (separated by commas, no dot at the end of the author list). Note also that the first author's name must be inserted in a separate field and all other authors’ names in another field.

Secondly, classify each reference article into the most suitable field, i.e. the most suitable Column of the DOD. To do this, find a menu box below the set form fields for the bibliographic data containing a string of codes, such as "e4/e229/e2387". Press the button that contains dots "…" located right-hand beside the field which contains the codes. A new window then opens containing the Branches of the DOD and the specific Branch and final Column where the Journal Article to which the reference you are currently importing belongs. By applying the links at the top of this window and the "+" links in front of the single Branches, you can move through the DOD within this window to search for the most suitable Column for the reference article. When you have found the suitable Column, mark it with a dot and click on "Insert" or "OK". The window then closes and a new code appears in the field beside the "…" button. This is the string of internal labels depicting the Branch of the DOD where the reference article will be inserted. You do not need to take note of this string.

Finally, once you have entered all fields of the set form for the import of the first reference article, click on the "Insert" button and wait until the website has reloaded. The set form, including the data for the first, already inserted article, is displayed again. Note that this article now exists in the DOD. Do not import the same article again! You can make sure if an article is already existent in the DOD by observing the comment "DOD Import Status: Available in DOD".

To import the next article from the reference list that belongs to the previously entered Journal Article, scroll down the window until you find an alignment of buttons containing Arabic numerals ordered from 1 to the maximum number of references, e.g. 40. Press button number 2 to import the next, in this case the second, reference article. Repeat this procedure until all, in this case 40, reference articles have been imported.

After you have imported the last reference article, complete the import simply by leaving the import function. Click on the DOD emblem at the top of the page or on another link at the left-hand menu to move to another area. Please note the final important tips:

Once you have begun to import the references of one Journal Article, always complete the import for all references before shutting down the import window. In other words, do not start the reference import for the same Journal Article twice.
Do not access again the import function of the particular Journal Article to which you have already imported the references and do not import twice.

To determine whether a reference list for a Journal Article has already been imported, refer to the reference list. If it has already been imported, DOD links appear behind each reference. Please note, it can take quite some time to process a complete reference list, i.e. to import the complete reference list of one Journal Article. This is because you need to research the bibliographic data and the abstracts (e.g. using Pubmed) as well as the correct full-text links (from the original publishers’ websites). In addition, any reference articles must be sorted into the correct and most suitable Branch and Column. Therefore, schedule some time (approx. 2 hrs) for the import of a complete reference list. If, in some cases, you cannot complete the import, leave open the window on your computer that contains the import function until you have completed the import. If this is not possible, you may in exceptional cases start the import function again later. Previously imported articles from the reference list must then be recalculated. This procedure can take between a few minutes and an hour, depending on the length of the reference list. Also, it cannot be guaranteed to be free from errors. For this reason, it is not recommended. In any case, wait until the recalculation of the references is complete before you continue with the import. If you note that some earlier DOD links no longer exist, do not import these reference articles again.

Moving Content Items within the DOD

Editors can move all Content Items belonging to any IC. To move a Content Item, the ZMI must be accessed. To access the ZMI, switch to your assigned Column which contains the item that should be moved. Apply the "Directory" link within the "Administration" link section to access the ZMI. You have then accessed the specific Column within the ZMI that contains the respective Content Item you may wish to move.

In the ZMI, scroll down until you find the Content Item to be moved. Apply the pull-down menu below the link "Edit Journal Article" (if the Content Item is a Journal Article) in the left-hand menu. Choose "Cut" and wait until the website has reloaded. Then go to the Column where the Content Item is to be placed and apply the pull-down menu directly above the intended position. Choose “Paste” and wait again until the website has reloaded. Then you can see that the item has been added to the new Column. Note that you can only move Content Items within your Columns. You cannot move an item into a Column to which you are not assigned as Editor. If you wish to move the Content Item out of your Column into another Column that is not your one, then move it into the "Miscellaneous Box" to which any Editor has the right to access. It is recommendable to look into the Miscellaneous Box from time to time in order to check if there are items suitable for the own Columns. Move these suitable items, which were put into the Box by other Editors, into your Column. Return to the DOD by applying the "Preview" button.

Creating a new Column below an advised Column

Approach the ZMI in the same way as described in the previous section. Scroll down with the window scroll bar at the outer right-hand side of the monitor until you reach the list of "Folders". Folders are Columns. To add a new, more specific Column below the Column you are advising, apply the pull-down menu of a Column below the link "Select Folder" directly above the intended position of the new Column. Select Folder” from the pull-down menu.

A set form opens. Enter the title you would like to assign to the new Column into the fields "Short Title" and "Title". Both of these fields must be filled with the same title (do not insert different titles or shorter titles). Fill only these two fields (and no other fields) and press the "Insert" button. Wait until the website has reloaded.

The inserted Column appears. To make the new Column visible on DOD, insert an empty text item. To do this, apply the pull-down menu called "Add to Folder" and select "Text". A text editor appears. Press "Insert" without entering anything in the text field. Return to the DOD by applying the "Preview" button.