Website Tutorial: Annotating Resources on Betacell.org

Last revision: May 6, 2011 by Thomas Houfek & J.-P. Cartailler

Scope of this tutorial
Starting Resource Annotation with the Resource Wizard
Completing Resource Annotation with the Resource Wizard
Modification of Contributed Resources

Scope of this tutorial

This tutorial covers how to create Resources on Betacell.org in general terms.

Resources come in a variety of Resource Types. Types currently supported are: Mouse, ES Cell, Antibody, Adenovirus, Functional Genomics Studies, Protocols, and Miscellaneous.

The kinds of metadata that desribe the Resource vary, according to the Resource Type. For example, one annotates the genetic alterations of a Mouse; and one specifies whether an Antibody is monoclonal or polyclonal. But one does not specify whether a mouse is monoclonal or polyclonal; nor does one describe genetic alterations of an Antibody. Therefore the tool we use to annotate Resources will behave a bit differently for different Resource Types: it will require you to fill out some different forms, depending on whether you are submitting a Mouse or an Antibody, etc.

This tutorial will not cover the particulars of the metadata that need to be entered for each of these types. Rather, it covers the general usage of the Resource Wizard to create a Resource, irrespective of type.

It must be noted, however, that Functional Genomics Studies are a special case. They are not annotated using the Resource Wizard, but instead must be prepared with the assistance of the Betacell Genomics team. If you contact us we will be happy to help you. But note that this tutorial does not apply to creating a Functional Genomics Study.

Also, if you are an Investigator or Affiliate participating in BCBC 3.0 (the third funding cycle of the Beta Cell Biology Consortium), you have some expanded features relating to Resources. Hence, some sections below will be flagged for the attention of BCBC 3.0 Members. Other users may ignore these sections.

It will be common for the annotation of a Resource to be completed across multiple user sessions, and possibly by multiple users (when a Resource is contributed on behalf of a Workspace.) Therefore this tutorial is divided into Starting Resource Submission, which explains the procedure for creating a "stub" of the Resource, and Completing Resource Annotation, which addresses completing the annotation of the Resource in general terms.

Starting Resource Annotation with the Resource Wizard

1. Go to the appropriate BCBC Resource Collection.

Your exact destination depends on the type of Resource you are creating, all of the Resource Collections may be accessed via links on the BCBC Resource Page. So if for example you intend to create a Mouse Resource, the appropriate Collection is the BCBC Mouse Collection.

BCBC 3.0 Members:

BCBC 3.0 Members who have a Laboratory Workspace or Core Facility Workspace have an alternative path to Resource Submission that in some ways is more direct:

Go to a Lab or Core Workspace in which you are a member.
Go to that Workspace's Lab Resources page.
Click on "Add a Resource" near the top of the page, invoking the "Add a Resource" popup.
Click on the Type of Resource you want to submit.

This effectively replaces steps 1-3 of these general instructions for Starting Resource Submission, so if you use this method you can skip to step 4, below. You may submit Resources using either method, however.

BCBC 3.0 Principal Investigators, Co-Investigators, and Delegates:

At the bottom of the General Information page you will see an additional control, labelled Add co-contributors. If you would like to designate another Workspaces as a co-contributor of the Resource, click this link and select the Workspace from the drop-down menu that appears. You may designate multiple Workspaces as co-contributors in this way.

2. Go to the "Submit a..." tab.

When you first navigate to the Collection page, there will be a view pane in which all the Resources are listed in the active tab, which is labelled Available Resources. To start submitting a Resource, click the neighboring tab, which is labelled "Submit a mouse strain" if you are submitting a Mouse, "Submit an Antibody" if you are submitting an Antibody, etc.

3. Click the "submission form to submit detailed information on..." link.

After the last step the active tab should be Submit an Antibody. At the top of the pane, there should be a link that reads "Please use the submission form to submit detailed information on an <resource type>". Click that link to launch the appropriate Resource Wizard. (The Resource Edit Wizard is just a component that leads you through a series of form submissions through which you annotate your Resource.)

If you are not already logged in, you will be prompted to do so at this time. (Resources may not be created by anonymous users.)

4. Fill out the form on the first page of the Resource Wizard: General Information

Each Resource is specified by a particular set of top-level metadata deemed appropriate to that Resource Type. This is entered using the form on the first page of the Resource Wizard. Depending on the Resource Type, some of the form fields may be Required. You will not be able to proceed to the second page until all Required fields are filled -- and importantly, your Resource will not be created until this first General Information form is successfully submitted.

If you have questions or difficulties with any of the fields on this form, please contact us for assistance. Occasionally we need to add options, selections, or fields to accommodate the full annotation of new submissions.

Once the General Information is successfully submitted, the Resource has been created, and you may if you like defer the rest of the annotation. Ordinary users should now see the new Resource listed in the Your resource submissions report, which is linked to by the BCBC Resource Contributions widget on the user's Dashboard.

You are now done with Starting a Resource Submission.

BCBC 3.0 Members:

At the bottom of the General Information page, you must select the Group to be Primary Contributor. Your choice is constrained to any Laboratory or Core Facility Workspace in which you are a member. For most laboratory Affiliates, there will be only one possible selection (and hence no real choice), but some members will have multiple possible selections here.

As with Resources submitted by ordinary users, submitting the General Information page creates the "stub" (the foundational record) for a Resource with the status of "In Progress/Private". However, for BCBC 3.0 members this status means that the Resource may be viewed and edited by any member of the workspace named as the Group to be Primary Contributor.

Why is this handled differently for BCBC 3.0 members?

to facilitate the collaborative annotation of Resources by the laboratories and cores presently active in the BCBC.
to allow other members of laboratories and cores to service Resource Requests
to allow the association of Resources with Deliverables assigned by BCBC Research Projects

The above considerations do not apply to Betacell.org members who are not participating in the BCBC 3.0. We nevertheless value the Resource contributions by these other members. We hope this explains why there is some bifurcation in how Resources are handled.

Completing Resource Annotation with the Resource Wizard

A complete Resource annotation is comprised of completion of all sections provided by the Resource Resource Wizard. Some sections are common to all Resource Types, and some are not:

1. The first page for any Resource Type is labelled General Information, and as mentioned above it must be completed to create minimal "stub" for the Resource.

2. Depending on the Resource Type there may be one or two more steps in the Resource Resource Wizard for specialized metadata. Like the various fields that may appear under General Information, these are beyond the scope of this general tutorial:

The Resource Wizard for Antibodies has a Uses step in which you can characterize multiple applications for the antibody, and an Images step in which you can upload associated image files.
The Resource Wizard for Mice has a step for annotating Genetic Alterations, a step for characterizing the Strain, and a step for uploading associated Images.
The Resource Wizard for ES Cells has a step for annotating Genetic Alterations and a step for uploading associated Images.

3. Irrespective of Resource Type, the Resource Wizard will always have the following steps:

Publications allows you to associate publications with the Resource.
Contacts lets you specify Contact People appropriate to the Resource.
Repositories lets you indicate from where the Resource (or related appropriate reagents) may be obtained.
Review summarizes information entered on previous pages, and allows you to Contribute the Resource to the BCBC Resource Collections if you so choose.

These steps occur in the Resource Wizard for all editable Resource Types, so they are covered by this tutorial. We will now explain each in turn.

Resource Wizard Publications step

In this step you associate any related publications to the Resource. If you already know the PubMed IDs for the publications you may enter them into the form's single text box (shown in Figure A). You may also enter search terms (for example, your last name). Then click the button.

Figure A.

You will then be presented with a list of results retrieved by your query (shown in Figure B). You then should put a check in the checkbox beside any publication you would like to associate with your Resource, and then click the button.

Figure B.

Note that whenever you do this our website must query PubMed. Unfortunately, PubMed enforces a daily limit on such queries which we occasionally exceed. If you experience a failure on this step, it may be due to this, in which case you will probably succeed if you wait a day and try again. If you have a persistent failure please do not hesitate to contact us.

Resource Wizard Contacts step

In this step you may associate up to two Contacts (Contact People) with the Resource: a Preferred Contact and a Lab Contact. These may be set to the same person by checking the box labelled Preferred contact same as Lab contact, shown in Figure C. For each Contact you may elect to name as Contact:

yourself, or
any other member of the Contributing Workspace, or
another Betacell.org member, or
a person without a Betacell.org account

In the first case, you need only select the Me (Your Name) option using the radio buttons. If you select Member of a contributing workspace, you then must select a member from a drop-down list. If you select Other member, you must type part of the member's name into a look-ahead search box, and then select the appropriate member from the choices that appear. In all these cases the Resource contact information will be drawn from the member's Betacell Profile (and it will automatically be updated when the information in the Profile changes.) If you select Other (indicating a person without a Betacell.org account), you must complete a short form with that person's contact information.

Figure C.

Resource Wizard Repositories step

This step is important because it tells other users how they might acquire the Resource (or an associated item like a reagent.) There are two general ways users may do so:

In some cases users may order the Resource or item from an external repository.
If a Resource is contributed by a Betacell.org Workspace, users may be able to Request the Resource using Betacell.org's Resource Request System.

Both possibile avenues are handled in this step. However, if you are not editing a Resource contributed by the Workspace of a group participating in the current funding cycle of the BCBC, you will only see the Associate this Resource with an external repository component. The Manage Workspace Inventory component will not appear. If you are editing a Resource contributed by a Workspace, you will see both components, as shown in Figure D.

Figure D.

Clicking on either link (Manage Workspace Inventory or Associate this Resource with an external repository) will expand the components. In their expanded state they will appear as in Figure E and Figure F respectively.

Associating the Resource with an external repository:

The expanded component for associating a Resource with an external Repository is shown in Figure E. To associate the Resource with a Repository, fill out the following form fields and submit by clicking the the

button:

Repository (mandatory). You must select the name of the repository from the drop-down list. If the Resource is available from a repository that is not listed, please contact us so that we can add that option to the list.
Stock Number (optional). If the Repository has a stock number identifying the Resource or related item, it should be entered here.
State (optional). Some Resources are available as reagents in different states. If the Resource is of a type for which we have defined states, you may select them from the drop-down list. If the Resource is available in a state that is not listed, please contact us so that we can add that option to the list.
BCBC only. If the Repository is the preferred source for BCBC members, this box should be checked.
Availability Notes (optional). Here you may enter any notes concerning the availability of the item.

You may associate multiple external repositories with a Resource. Also, with multiple entries you can indicate that the Resource is available in multiple states (probably under different Stock Numbers) from the same Repository.

Figure E.

Managing Workspace Inventory

The following section is only relevant to BCBC 3.0 members. Other users may skip to the Resource Wizard Review step

Resources that are contributed by the Workspaces associated with groups active in the current funding cycle of the BCBC may be made available through Betacell.org's Resource Request System. The Manage Workspace Inventory component of the Repositories step of the Resource Wizard is one place where you may define Inventory Items related to Resources, so that those Inventory Items may be made available for Resource Requests.

Inventory Items may also be managed on the Lab Resources or Core Resources page of the Workspace that contributed the Resource, but that is beyond the scope of this tutorial. The form for Managing Workspace Inventory is shown in Figure F. As you can see, it is very similar to the form used to associate the Resource with an external repository (described above.) And it works in precisely the same way, except for minor differences in its fields. The fields are:

Stock Number (optional). If the Repository has a stock number identifying the Resource or related item, it should be entered here.
State (optional). Some Resources are available as reagents in different states. If the Resource is of a type for which we have defined states, you may select them from the drop-down list. If the Resource is available in a state that is not listed, please contact us so that we can add that option to the list.
MTA. You may select any relevant Material Transfer Agreement (MTA) files from the drop-down list. These MTA files must be uploaded by the Investigator who administers the Workspace that contributed the Resource.
Availability Notes (optional). Here you may enter any notes concerning the availability of the item.

Note that there are two controls appearing in Figure F that did not appear on the Associating the Resource with an external repository form: an edit button (

) and a delete button (

). They appear because this screenshot depicts a Resource with a single Inventory Item. (This may be hard to make out because it has no Stock Number or Availability Notes.) Figure E depicts a Resource with no repository associations yet. If it had repository associations the edit and delete buttons would appear on that form as well.

Figure F.

Resource Wizard Review step

This is the always the final step in the Resource Wizard, and for the most part it is self-explanatory. It assembles the information entered in all the prior steps into a single page, so that it is easier for you to review the information that you have entered. However, this is also the page on which you may elect to contribute the Resource to the BCBC Resource Collections.

At the bottom of the page ordinary users (that are not active participants in the BCBC 3.0) should see a big button labelled . If you would like to contribute the Resource, click this button.

BCBC 3.0 members: Resources contributed by BCBC 3.0 Workspaces may be edited by any member of the Workspace, and any member can contribute them to the BCBC Resource Collections. Before doing so, however, you should make sure this is what your workspace leader (Lab Leader or Core Director) wants you to do.

Clicking this button will raise the pop-up shown in Figure G. You must select which class of users you would like to be able to view the Resource.

Other users will be able to view the minimal information in the listings of the BCBC Resource Collections but will be unable to view the Resource in detail, nor will they see who contributed the Resource. This is to ensure that Investigators who wish to share Resources with other BCBC members are not put in the position of responding to inquiries about the Resource from users not in the BCBC.

If you like, you are certainly encouraged to make the Resource available to the Public. All users will then be able to view the Resource details, including what user or Workgroup contributed the Resource.)

Figure G.

Modificiation of Contributed Resources

After a Resource is contributed, users who previously had privileges allowing them to edit the Resource will no longer be able to do so.

Instead, they must request a modification be made by the curators of the BCBC Resource Collections. For contributed Resources the Request an edit link will appear in the Resource Access section at the top of the Resource Detail page (the page you see when you click on a Resource listing in any of the BCBC Resource Collections, assuming you have permission to view the Resource.)

BCBC 3.0 Members:
From the Contributing Workspace of the Resource, its Inventory Items may still be managed on the Lab Resources or Core Resource pages of the workspace. There are plans to allow Workspaces to continue to maintain other details concerning the Resource (Contacts and Publications), but currently you will have to Request an Edit to update these sections.