StemDB Manual

(Last Update: 09 May 2011)

Introduction [ToC]

The Stem Cell Database (StemDB) aims to be a comprehensive resource for stem cell information and stem cell expression data. The StemDB database is built initially as a repository for stem cell information generated by the EuroStemCell Consortium, an EU Framework 6 Project, and work has continued under the EuroSystem Project. The database allows appropriate access to the consortium data for the wider scientific community. StemDB is capable of storing information regarding cell-lines, antibodies, cloning vectors, primers, protocols, rodent strains, recombinant proteins and published references or in-house documents. A second phase of the projects adds support for gene expression profiling data and the tools to query this data.

Through the StemDB web interface it is possible to input / query / edit information about the biological entities stored. Furthermore, users can initiate and join collaborations between users and user groups and share data amongst each other. Additionally, the web interface also allows users to input and manipulate project management data that is used within the individual work package or flagship projects within these collaborations.

Registering: While data retrieval for all public records is available from within the StemDB interface without the need to obtain a user account, it will be necessary to register in order to submit and manipulate data, to enter collaborations and to view restricted data. Registration is free of charge. To sign up for a user account click here.

Support for bulk data submission: In order to support bulk upload of data a number of database-compatible Excel forms are available. Please click here to download the database compatible Excel forms. Once the data has been collected by individual labs, the Excel forms should be submitted for inclusion in the database by emailing the completed forms to stemdb_admin. [If your submission exceeds 10MB then please contact stemdb_admin before submitting your data via email].

Fig. 1: A (massively) simplified schema of StemDB.

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User Accounts, Groups and Collaborations [ToC]

While data retrieval for all public records is available from within the StemDB interface without the need to obtain a user account, you will need to register for a user account in order to gain access to the advanced features of StemDB like data submission and project management features.

StemDB organises users in three layers of increasing abstraction to facilitate data sharing and collaboration: Users, User Groups and Collaborations. The ER diagram below (Fig. 2; this is just for users with an added interest in the structure of StemDB and of no significance to the day-to-day use of StemDB) lays out the conceptual relations between these three classes.

Fig. 2: Users, Groups and Collaborations in StemDB.
1. User Account
  
  Each registered StemDB user will be assigned a user account. This account uniquely identifies the user within the StemDB system and will allow the user to become the member of user groups and collaborations in order to support data sharing and advanced collaboration. Additionally, the user account enables StemDB to keep track of the ownership of records submitted to the database. For further information on how to modify your user account have a look at the help for the accounts main page.
2. User Groups
  
  Users belonging to the same research group are encouraged to from a user group within StemDB. Every user can start an own user group from the account and group settings page and subsequently invite other registered StemDB users to join the group. Alternatively, user may request membership in existing user groups. These requests have to be granted by the leader of the group. By default, the user that created a group will become the group leader, but later on additional users can be made group leaders by the existing group leaders. Furthermore, group leaders can update general information about the group and also remove users which have left the group. For further information on how to modify your user group settings have a look at the help for the accounts main page and the user group page.
3. Collaborations
  
  On top of the user group concept, StemDB provides an additional layer to facilitate data sharing and cooperation amongst users, termed 'Collaborations'. Collaborations allow individual users and whole groups to join efforts. Similarly to groups, collaborations can be initiated by every registered StemDB user. The initiating StemDB user will become a manager of the new collaboration and subsequently new users or whole groups can be invited to join the collaboration (the users or group leader will have to accept the invitation). Of course, users can also request to join a collaboration (the requests have to be granted by one of the collaboration managers). For further information on how to modify your collaboration settings have a look at the help for the accounts main page and the collaboration page.
  
  Within collaborations, their managers can define projects and work packages. Please refer to the project management section for further details.
  
  In order to maintain a high level of quality for all data submitted to StemDB, we have restricted data submission to members of certain, approved collaborations. By default, collaborations do not have data deposit rights, but every manager of a collaboration can request deposit rights by emailing the StemDB administrators.
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Data Retrieval and Submission [ToC]

StemDB provides a large body of data related to stem cell research. Users can not only browse and retrieve the data already available in StemDB (subject to access permissions), but also submit their own data in order to share it with their collaborators and/or the wider academic community. Data submission is restricted to members of approved collaborations in order to limit the submission to quality data only.
1. Data Search and Retrieval
  
  Searching the entries you are interested in within StemDB is easy: Simply select the sort of data you are interested in from the 'Data Query' menu and you will redirected to a page that lists all the StemDB entries of this kind. You will be provided with a search mask ('Filter Criteria') that allows you to further specify the specific entries you would like to be shown. You can use a combination of various data type specific fields to limit the search results to your interests. The list of entries displayed will be dynamically updated to match these criteria. By clicking one of the search results you will then get more details about this entry and you will have the option to see the full details and to edit the entries (that is, if you are the submitter and have permission to modify it).
  
  Alternately, use the web-style search engine to search StemDB entries. You can access this by clicking the 'Search' option in the Data Query page or directly using the Search box on the Home page. This provides you with a flexible, web-style search tool with a flexible query language and, when browsing results, a faceted, filter system to allow you to narrow down your search to specific data types easily.
  
  For further information on how to use the StemDB search features have a look at the help for the data query page.
2. Data Submission and Editing
  
  All StemDB users are encouraged to submit their own data to StemDB. However, data submission is restricted to members of approved collaborations in order to maintain a high level of quality of all StemDB data. This means, that you will have to be a member (or a member of a group that is a member of) a collaboration that has been granted data deposit rights by one of the StemDB administrators before you can submit any data.
  
  To submit an entry, you will have to be logged in to your StemDB User Account. Simply select the kind of data you would like to submit from the 'Data Input' menu and you will be redirected to a form page that allows you to enter various information. Some of this information will be required in order to proceed with your submission, other might be optional.
  
  When you are content with the data you have entered, you can proceed to the next step, which will take you to an overview page of the data that you just entered. Note, that at this point no data has been submitted to the database yet! You can now review the data you have entered and correct any mistakes you might have made before. Furthermore, it is possible to link other StemDB entries (either existing ones or new ones which you can create 'on-the-fly'). We would like to encourage you to take some time to associate all entries that are sensibly connected to your new submission at this stage.
  
  Once you are finished and satisfied with all data you have entered and all associations you have made, you can finish the submission by clicking the appropriate button in the interface. Your data will now be inserted into the database and after a few seconds you will be re-directed to a query page amongst whose search results you should be able to detect your new submission. Of course, it is possible to modify the submitted data at any time after your submission.
  
  Figure 3 below gives the rough overview about the workflow for data submission to StemDB. For further information on how to submit data to StemDB have a look at the help for the data submission pages.
  
  Fig. 3: Typical 4-step submission process.
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Project Management [ToC]

In addition to standard data submission and retrieval, StemDB provides an interface for advanced project management facilities. Users that join efforts in a Collaboration are able to work on common projects, for which they can submit reports to StemDB, therefore allowing other collaborators to keep track of the current state of a project.

Project Creation: Users that manage a collaboration are able to create new projects within this collaboration. Specific groups within the collaboration can then be assigned to the individual projects and more specific objectives, deliverables and checkpoints can be declared.

All users in the groups that have been assigned to a project can view and submit reports for the objectives, deliverables and checkpoints of the projects. Additionally, all group leaders participating in the same collaboration as well as the collaboration managers have read access to the records and SATs. Submitting a report is essentially the same as submitting any other type of data to StemDB and further information can be found here.

For further information on how to use the StemDB project management (including Marratech and other web conference software support) features have a look at the help for the project management home page.

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StemDB Functionality by Page [ToC]

General Pages
- StemDB Home
  
  This is the home page of StemDB and therefore it is most likely the first StemDB page that you have seen. Apart from some general information about StemDB, you will also see current notifications concerning your user acocunt (e.g. if you have been invited to join a user group) and some statistics showing the different types of data available within StemDB and how many records of each kind have been submitted.
  
  The top-right of the screen (just below the StemDB logo) displays some information about the User Account you have logged into, or -- if you have not logged in yet -- links to the login and registration pages. The top-left part of the screen is reserved for the navigation menu. Using the links in the menu you can reach the search, data submission and project management features of StemDB (note, that the latter two will only be available if you have signed into your account).
  
  Fig. 5.1: A screenshot of the StemDB home page after logging in. The most important functional parts are highlighted.
- Security Certificates and Security
  
  In order to guarantee the security of your private data, all communication between the StemDB servers and your local computer will be carried out using an encrypted SSL connection, once you have logged on to StemDB. In the past it was necessary to install security certificates from StemDB into your local web browser. This is no longer the case as StemDB now uses a trusted, CA Signed SSL certificate which all modern web browsers should recognise automatically.
- Log-In Page
  
  This page allows you to log in to your StemDB User Account. There are two text fields which are meant for you to enter your username and password respectively. If you have not obtained an account yet, you can register free of charge. If you forgot your username and/or password, you can request these information to be sent to your email address (please follow this link; see also the highlighted part of Fig. 5.2).
  
  In order to complete the login process, you will furthermore have to accept the general terms and conditions that apply to StemDB.
  
  Fig. 5.2: A screenshot from the log-in page.
- User Registration
  
  The form on this page allows you to sign-up for your own StemDB User Account. You will be asked to supply some basic information about yourself and most importantly an email address. It is essential that this email address is valid, because your initial password will be send to this address. Consequently, you will not be able to log into your account unless you can receive StemDB's confirmation email.
  
  You will furthermore be asked to provide a desired username. This can be any name of your choice, but generally it has established as a good convention to use the first letter of your first name(s) together with your last name. Note that usernames in StemDB have to be unique, therefore we might take the freedom to append a number to the username you entered if it already existed in StemDB. You can change your username later on from your account settings.
- Bad Access
  
  It seems like you have tried to access a page that you are not allowed to access. If you think this is due to an error in StemDB, we would like to encourage you to report this issue to our support team.
- Database Problem
  
  While we take every effort to ensure that StemDB remains fully functional at all times, occasionally something might go wrong. StemDB is under constant development and sometimes minor issues might slip our mind. It seems you have encountered one of these issues. We apologise for any inconvenience caused, but would like to encourage you to report the issue to our support team so we can take care of it. Please try to report the exact circumstances that lead to the error.
- Log-In Required
  
  It seems you have tried to access a page that is only accessible by registered StemDB users. Please log-in to your user account (or register with StemDB to obtain a free user account if you have not done so already) before you return to this page.
- Log-Out
  
  This page confirms that you logged out from your StemDB user account. You can now continue browsing the public content of StemDB, log in again or continue browsing the web outside StemDB. Thank you for using StemDB and we hope to see you again soon.
- Forgot Password
  
  If you have forgotten your username and/or password, you can enter you email address into the designated field (the same email address that has been registered with your StemDB user account) and request for your username and a new password to be sent to your email account.
- Error
  
  While we take every effort to ensure that StemDB remains fully functional at all times, occasionally something might go wrong. StemDB is under constant development and sometimes minor issues might slip our mind. It seems you have encountered one of these issues. We apologise for any inconvenience caused, but would like to encourage you to report the issue to our support team so we can take care of it. Please try to report the exact circumstances that lead to the error.

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User, Group and Collaboration Pages
- User Account Main Page
  
  The user account main page is the hub for all user-related matters. On the top of the page, you will have the option to modify your personal data, username (subject to availability of the username) and password (see the highlighted area in Fig. 5.3).
  
  Just below your personal account details you find a logo indicating your level of submission (or "deposit") rights within StemDB. Please refer to the user, groups and accounts section for further information.
  
  The main functionality of the user account main page, however, comes with the panels below. How exactly these panels will look like depends on your memberships in groups and collaborations, but the overall idea remains the same in either case: Spread across several panels you will find all the information you might ask for regarding the user groups and collaborations you are involved in (of course, if you are, say, not a member of any collaboration the corresponding panel will be hidden to avoid confusion).
  - User Group Memberships Panel:
    
    If you are already a member of one or more groups, StemDB will display some basic information about these groups in this panel. Besides the groups' names, you will see information about their research area and address, your status within the group (i.e. whether you are a group leader or a regular member), a list of all other members of this group (and of all people who have requested or have been invited to join the group) and a list of all the collaborations the group is involved in.
    
    Of course, you can leave a group at any time by clicking the corresponding link below the group information ('leave this group') or beside your name in the group members list. If you are a group leader, you can additionally modify the group's description, remove existing members or promote them to group leader status (links 'remove' and 'promote' next to the respective member in the group members list), accept or decline membership requests, invite new members or request to join further collaborations.
    
    N.B. If, at any point, all group leaders leave a group, the group will be removed from StemDB.
  - Collaboration Memberships Panel:
    
    If you are a member of one or more collaborations or one of the groups you are a member of is involved in a collaboration, StemDB will display some basic information about these collaborations in this panel. Besides the collaborations' names, you will see a general description, your status within the collaboration (i.e. whether you are a manager of the collaboration, or a regular member -- either via direct membership as an individual or via a group membership), a list of all other members of this group, which is divided into three parts: existing individual members of the group, groups that are members (this in turn is an extensible panel, as these lists tend to get rather long for large collaborations) and a list of pending memberships.
    
    If you have joined the collaboration as an individual (rather than via a group membership), you may leave the collaboration by clicking the link below the collaboration information ('leave this collaboration') or beside your name in the members list. Moreover, if you are interested in a complete list of all people involved in the collaboration, you should follow the 'complete list of ALL users and groups' link.
    
    Further actions are available to collaboration managers: You may remove existing members or groups, promote individual members to manager status, accept or decline membership requests, invite new groups and members or modify the collaboration's description and name.
    
    N.B. If, at any point, all collaboration managers leave a collaboration, the collaboration will remain in StemDB as a legacy, but nobody will be able to admit new members into the collaboration or take administrative actions of any other kind.
  - Pending Memberships Panel:
    
    This panel displays information on all your outstanding group and collaboration memberships. If you have been invited to join a group or collaboration, you can choose to accept the invitation or to decline it. Additionally, you will also find a list of all the groups you have requested to join (if any) and have the option to withdraw your request.
  - Group/Collaboration Creation Panel:
    
    The last panel provides you with the means to create new groups and collaborations or to join existing ones.
    
    You can browse through lists of all existing groups and collaborations and filter them dynamically by entering information in the text fields above the list to locate the ones you want to join and then click their name to request membership. The corresponding group or collaboration leaders will be notified of your membership request and can then decide upon it. You can review all your open requests in the pending memberships panel.
    
    Every registered StemDB user has the right to create new collaborations and user groups, however, in the most cases user groups should reflect research groups or departments within an institution, so most user will probably never have to create a group themselves. Similarly, collaborations mostly correspond to large international consortia or larger institutions, so again, only a limited number of users will ever have to create a new one. Nevertheless, creating groups and collaborations is simple! Just click the corresponding link in this panel and you will be guided to a page where you can enter some basic information about the group / collaboration you want to create.
- Change Password
  
  This page allows you to enter a new password for your user account. You are required to enter your new password twice in order to make sure that there are no typos (which could possibly lock you out of your very own user account!).
- Create User Group
  
  In theory, every registered StemDB user can create a new User Group. While these are primarily intended to join members of the same department or research group, if you feel it is adequate to establish a user group on other grounds, please feel free to do so.
  
  The page requires you to enter some very basic details about the group, firstly a name to identify the group in StemDB and also a short description and an address (an affiliation will do). Once you submit this information, you will automatically be made a group leader of the new group and you will be able to locate it in your user account main page, from where you will be able to administrate the group and add members to it.
- Create Collaboration
  
  In theory, every registered StemDB user can create a new Collaboration. While these are primarily intended to join members of a consortium or other international project, if you feel it is adequate to establish a collaboration on other grounds, please feel free to do so.
  
  The page requires you to enter some very basic details about the collaboration, firstly a name to identify the group in StemDB and also a short description. Once you submit this information, you will automatically be made a manager of the new collaboration and you will be able to locate it in your user account main page, from where you will be able to administrate the collaboration and add members and groups to it.

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Data Input Pages
- Data Submission Main Page
  
  This page serves as an entry point to the data submission process for StemDB. The functionality it provides is very basic and straightforward: You will find a drop-down list of all StemDB data types. Choose the kind of data you would like to submit and you will be forwarded to the respective data input page.
- Submit or Modify Entry
  
  This is the primary data submission page for StemDB. Of course, the exact contents of this page depend on the specific type of data you would like to submit to StemDB, however, the overall layout and the principles of use are always the same. Fig. 5.6 displays a screenshot from the document submission page, for example.
  
  All submission share some common properties: Each submission to StemDB will be issued with a unique and stable accession number that can be used to identify this record. The accession number will be automatically attached to your record upon the first submission (but it will remain unchanged when you update the record later on).
  
  Furthermore, you can set the access permissions for each record you submit to StemDB by choosing all collaborations that you would like to be able to view your submission from a list menu (cp. the section labelled "Access Permissions" in Fig. 5.6). All collaborations and groups that you are involved in will show up in this menu. Select either one or a combination of them to define the access restrictions. Alternatively (and we would like to encourage you to do so), you can make your submission viewable by everybody (PUBLIC). Lastly, you can keep submission private (i.e. only accessible by yourself) by deselecting all collaborations.
  
  Fig. 5.6: A screenshot from the Document submission page.
  
  Depending on which type of data you are about to submit, you will have a number of form fields that allow you to enter data about the submission or to select from a range of pre-defined values. Some of these fields are required to proceed with your submission. Upon submission these fields will be highlighted red if they are missing. This will ensure that no entries lacking crucial information are submitted to StemDB (cp. the section labelled "Mandatory Field" in Fig. 5.6). Input fields that have been filled with valid information, on the other hand, will be highlighted in green.
  
  Once you have entered all the data for the new entry, you can proceed to the next step, which will take you to an overview of the whole submission. Please be aware that no data will be inserted into StemDB at this point yet! You will have to confirm your submission at the next page before your new entry will be submitted!
- Associate Existing Entries
  
  You will be redirected to this page, if you decided to look for existing StemDB entries to associate with your StemDB submission. The page provides you with a simple query interface that allows you to browse through all entries (that are accessible by you) of the selected type, to view some information about them and (if you decide to do so) to associate them with your main submission. Use your browser's back button to return to the submission overview page.
  
  The page is essentially the same as the main query page. Depending on which kind of data you are looking for, you will have a number of input fields that allow you to refine your search. All entries matching these criteria will be displayed in a table, from which you can choose to display more information about the entry by clicking a row or to associate the entry of interest by clicking the edit icon ().
  
  Fig. 5.7: A screenshot from search page for associations.
- Associate a New Entry
  
  If you decide to associate a new entry of some sort to your primary submission, you will be redirected to a page which looks very similar to the primary submission page. Similarly, you will get a number of form parameters specific to the data type of the entry to be associated along with some general submission properties.
  
  Please refer to the manual for the submission page for further directions.
- Submission Overview Page
  
  This page provides an overview of the data submission at hand. Please take a moment to review all the data you entered. No data has been submitted to StemDB yet! If you detect a mistake click the "Modify Submission" button to return to the data input page.
  
  Additionally, you can associate other StemDB entries with your new submission. You can either associate a new entry (enter the data as you go along) or existing entries (browse StemDB and select which entries to associate). The submission page features two drop down lists for this purpose from which you can chose which type of data to associate. Existing associations will be displayed in a tabbed panel.
  
  Fig. 5.8: A screenshot from a submission overview page.
- Submit or Edit Marker Pattern
  
  The submission page for marker patterns differs slightly from the standard submission page. In addition to the usual form input fields, you will have find features that allow you to define the marker pattern itself.
  
  The idea behind marker patterns is fairly straightforward: Biological markers (as the name suggests) mark certain states or parts of cells or whole organisms (we call the things that are marked "conclusions"). Sometimes it is only valid to draw these conclusions given that a number of conditions hold, e.g. a certain antibody might mark cancerous cells, but only in a specific tissue type, while it is not valid to draw any conclusions in other tissues. If the marker works in any case (to the current state of knowledge), you can leave the conditions empty. Furthermore, you might also be able to draw "negative" conclusions in some cases, e.g. that given you found the marker in a cell, you know that this cell can NOT be a stem cell.
  
  The StemDB supports two forms of data input in order to define marker patterns:
  - You can browse a number of ontologies (from the OBO Foundry project) for the terms you would like to use in the conditions and conclusions of the pattern (cp. Fig. 5.9 "Browse Ontologies"). This is the preferred way of describing your marker pattern, because it supports a common, shared vocabulary and will therefore make your pattern more useful to other researchers (and also to yourself, since you will be able to better understand their descriptions).
  - If you cannot locate any term matching what you would like to describe, you furthermore have the possibility to add a custom term (cp. Fig. 5.9 "Add Custom Terms"). Upon submission of such a term, StemDB will once more try to match the term you entered to our supported ontologies and associate that instead, if found, or otherwise insert it into StemDB.
  Whenever you add a term, regardless of whether you are using an ontology or entering the term yourself, make sure to specify whether the term belongs to the conditions or the conclusions of the pattern and whether it is positive (marking what is the case) or negative (marking what is not the case).
  
  Fig. 5.9: A screenshot from the marker pattern page.
  
  Lastly, you can get some additional details about the terms you added to the pattern by clicking the term's ID (cp. Fig. 5.9 "Term Details"). StemDB will make use of the EBI's Ontology Lookup Service to attempt to retrieve further information about the term at hand. If, at any time, you find that a term you added should not belong to the pattern, you can, of course, remove it by clicking the "X" button next to the term.
- Submit or Edit Experimental Annotation
  
  Submitting a gene expression experiment involves an additional step as compared to the standard submission process: After you have entered all the general information about your experiment, you will be forwarded to the page at hand where you will be asked to provide some elementary sample annotation for the subjects of your study.
  
  The page (cp. Fig. 5.10) essentially consists of a table, in which each row represents one of the samples in your study and each column represents a parameter with which you can describe the sample. Additionally, you will see lists of all the files that are contained in the experimental data archive that you submitted in the previous step.
  
  Initially, the table will contain just as many rows (samples) as there were files in the archive you submitted (up to a maximum of 10 samples will be added initially). This is based on the assumption that each of the files contains the data for one sample, however, you can dynamically add or remove rows (samples) to suit what is actually the case. Each row contains a select box which lists all the experimental data files that you have uploaded with your experiment (cp. Fig. 5.10 "Link Files"). You should select all the files that report data for each sample. For example, standard Affymetrix microarray experiments will yield one file per sample, so you should associate one of the files to one sample each. Other technologies might yield only one file for two samples (e.g. two-channel microarrays for which you should associate the same file to two rows of the table) or alternatively more than one file for the same sample (associate all multiple files to the same row, in this case).
  
  Moreover, you can dynamically add columns (parameters) to the annotation table. By default, three parameters will be added to the annotation (Sample Name, Species and Sex), but you can remove or rename any of these or add parameters from a list of pre-defined values (inspired by common annotation standards) or enter parameter names yourself (cp. Fig. 5.10 "Add Parameters").
  
  When you are content with the annotation entered, you can click "Submit Sample Annotation" to proceed to the submission overview page.
  
  Fig. 5.10: A screenshot from the experimental sample annotation page.
- Submit or Edit Data Analysis Results
  
  A further step may be taken on submitting a Gene Expression Experiment in order to upload data analysis results into StemDB. Once General Information and the Experiment ZIP file annotation are complete, the option exists to upload Experiment Analysis Results into StemDB. When we talk about “experimental analysis results” here, we mean any sort of results from your data analysis that can be represented in a table, where each row stores information about a certain gene (or probe) in your data.
  
  Once the sample annotation is complete the submission process will return you to a display page in StemDB to allow you to review your submission:
  
  Fig. 5.11: Summary of a Gene Expression Experiment Submission
  
  Use the ‘Associations with Other Database Entries’ option to select ‘Data Analysis Results’
  
  Fig 5.12: Detail selecting associated Data Analysis Results
  
  You then get a small option screen where can you enter some general information about the results. The analysis results file needs to be a plain text file with columns separated by TAB's. Note the option to map the data analysis results to a gene annotation data set
  
  Crucially, you need to select the appropriate reference dataset for the organism you are studying.
  
  Fig 5.13: Detail submitting General Information on Data Analysis Results
  
  Once complete, click ‘Parse Results File’ to proceed to annotate and describe the table details
  
  You are then presented with a selector which allows you to map to the gene annotation data set on the next display, followed by the means to select which columns from your data set to include in the analysis results. You can edit column labels and descriptions to describe the data in the table you have uploaded.
  
  It is necessary to select a column to act as an ‘Accession’ (key) value in the dataset to map to the gene annotation data sets. The values of this column will be used to establish a mapping between the data you uploaded and the reference dataset you've chosen earlier. Also, make sure to select the column(s) in the reference dataset to use for the mapping:
  
  Fig 5.14: Annotating Data Analysis Results
  
  Note that you can use the first row in your data file as a ‘header’ using the checkbox at the bottom of the form.
  
  Fig 5.15: Using the first row of the tab delimited file as a header
  
  Once you submit this form, the data set is parsed by the system and you are presented with a selection tool where you can define the columns you wish to display in this data set, and the order in which they are displayed. The selection box (on the left) shows all available columns, so you have to select the columns required for display from both the annotation data sets and the data you uploaded.
  
  Fig 5.16: Sorting and selecting default columns for display
  
  Note that the other data elements will still be available for users to browse using their own custom display selection.
  
  Completing this form completes the submission process, and you will be returned to the preview screen with a small summary of your data analysis results visible.
  
  Fig 5.17: Summary Preview of Data Analysis Results
  
  When you submit the Gene Expression Experiment, you will be returned to the browse screen for the Gene Expression Experiment data type. Browse to your results and you will be able to preview and view your data analysis results as you defined them above.

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Data Retrieval Pages

Data Query Main Page

This page serves as an entry point to the data retrieval process for StemDB. The functionality it provides is very basic and straightforward: You will find a drop-down list of all StemDB data types. Choose the kind of data you would like to search and you will be forwarded to the respective data search page.

Alternately, the Search box provided can be used to directly access the “search engine” style functionality within StemDB.

You can use StemDB's search tool to quickly search all the entries in StemDB that cover a topic of your interest. Simply enter a search term in the designated text field and press enter. You can search for individual words or phrases or use the query language provided to create a more specific search. StemDB will search the various data types, including the full text of any attached documents, in order to access the data you require. Note that you can also filter the results provided by document type. On the right-hand side of the screen the filter tool shows the number of document types in each category that match your search, and allows you to filter the results further by selecting and de-selecting the checkboxes for the various types.

Please note that the documents you will be able to access will be limited by your access permissions within StemDB. As a guest user, or when not logged in, you will only be able to browse public data.

A powerful query syntax is included in StemDB search functionality. Please see the below table for a brief guide to the syntax involved.

Query	Matches...
Pou5f1	Matches the term ‘Pou5f1’ in common fields in the entry.
Pou5f1 Nanog Pou5f1 OR Nanog	Matches the term ‘Pou5f1’ or ‘Nanog’, or both, in common fields in the entry.
+Pou5f1 +Nanog Pou5f1 AND Nanog	Matches both ‘Pou5f1’ and ‘Nanog’ in common fields in the entry
author:Smith	Matches the term ‘Smith’ in the author field in the entry.
author:Smith -abstract:nanog author:Smith AND NOT abstract:nanog	Matches the term ‘Smith’ in the author field, and doesn't have the term ‘nanog’ in the abstract field.
(Smith OR Jones) AND nanog	Matches the term nanog and also the terms ‘Smith’ or ‘Jones’ or both.
Smith*	Matches all terms that start with the text ‘Smith’, including the text itself.
Bus~	Matches all terms that are close to the word ‘Bus’, Such as ‘Mus’
"ES Cell"	Matches the exact phrase “ES Cell”, in common fields in the document.

The field names used for StemDB data values are detailed in this document in the Appendix.

Please note that Gene alias synonym parsing is included in search system. Also note that OR is the default logical operator.

Fig. 5.18: A screenshot from the StemDB Search engine.

Browse Entries

Explorative data retrieval in StemDB is simple and straightforward! The search page provides you with some easy-to-use functionality which is meant to help you to locate and view the information you are looking for.

Fig. 5.19 displays a sample screenshot from the Document browse page. Other browse pages vary slightly (because the data to be shown obviously depends on the kind of data you are looking at), but nevertheless the principal layout of the search page is always the same.

In the centre of the page you will see a table displaying all StemDB entries of the enquired type that have been made accessible to you. If there are more than a certain number of entries, these will be split over several pages to avoid overloading of the page. Please use the links directly below the table to navigate between pages. When you click a row in the table, you will get some additional details to be displayed in the box below it.

You can then click the view symbol () to jump to the full details page for this entry or, if you are the submitter of the entry, the edit symbol () to edit any record of the table. Moreover, clicking on the name of a user in the table will open a small popup dialog that will detail further information about the submitter of the record.

Of course, it might be hard to locate the entries you are looking for only by browsing through the table of all records. Therefore you will furthermore find a number of form fields (cp. Fig. 5.19 "Browse Options") that allow you to dynamically narrow down the entries displayed in the table to only those matching the criteria you defined.

Fig. 5.19: Screenshot from the Document browse page.
View Entry

This page displays all information that has been submitted for a certain record in StemDB. Additionally, you will find several tabs for all entries that have been associated with this record on the bottom of the page (if any).

Furthermore, you can obtain information about when the entry has been submitted and about the user who submitted it (cp. Fig 5.20"Submission Info").

Notably, you have the option to export all the data for this record to various popular file formats. Currently, StemDB supports export to a printer-friendly PDF file format and to the computationally usable XML file format (cp. Fig. 5.20 "Export Options").

If you are the submitter of the entry shown, you will also have the opportunity to proceed directly to the data modification page.

Fig. 5.20: A screenshot from an exemplary data display page.
Advanced Marker Search

While you can search markers in the standard way, you might find it more useful to look for markers in term of what they are good for. The advanced marker search page provides you with the means to do so.

You can specify all the conditions and conclusions (cp. marker pattern submission) that you would like to see in the marker (or also conclusions and conditions you would not like to see!), give some restrictions on the name of the marker and limit results to markers applicable in certain species (please note that search results will have to be applicable in all of the selected species, so the more species you select the less results you will get) or of a specific type (results must by any of the selected types).

For example, the search shown in Fig. 5.21 would look for all antibodies marking Parkinson's disease in human (which will, unfortunately, not yield any results).

Fig. 5.21: A screenshot from the advanced marker search page.
Advanced Marker Search Results

The results of the advanced marker search will be shown on this page. The results will be displayed in a way similar to the main query pages: On the top of the page you will find a table containing all markers matching your query. When clicking a row of the table, additional results will be shown in the box below. Furthermore, you can use the view () and edit () symbols to navigate to record-specific pages.

[Return to Table of Contents]

Project Management Pages
- Project Management
  
  This page is the entry point for the project management section of StemDB. You will see a table displaying all projects that have been registered with StemDB in any of the collaborations you are involved in along with which research groups have been assigned to these projects. Users within these groups can submit reports for the project and display a situation analysis table (SAT). The managers of the respective collaborations will furthermore have the opportunity to modify the general details of the project and to define its SAT (by defining objectives, checkpoints and deliverables).
  
  Moreover, if you are managing a collaboration, you can register a new project within it by selecting the name of the collaboration from the respective combo box.
  
  We understand that many people are using various web conference software (e.g. Marratech) to manage potentially large projects. It can be desirable to use this software to jointly browse websites, like StemDB's project management interface, but unfortunately, the browsers integrated into the conference software are often very old and do not support modern, dynamic web pages. We have therefore created a simplified version of the project management features in StemDB (data retrieval only) that should run even in older browsers. You can access this feature here: http://www.stemdb.org/stemdb/stemdb/marratech.
- Display Situation Analysis Table
  
  The situation analysis table (SAT) is meant to be a convenient way for all people involved in a large, on-going project to assess the current state of the project and to see which checkpoints have been reached already, which objectives have been achieved and which are still outstanding.
  
  Fig. 5.22 shows a SAT for a sample project. Checkpoints and deliverables which are overdue or have been submitted late will be highlighted in red, while those submitted in time will be highlighted in green (cp. section "Project Timing" in Fig. 5.22). Hovering over a row in the table will preview the abstract of the respective report and when you click the view symbol () you can get the full details of this record.
  
  You can furthermore export a complete overview of the project to a printer-friendly PDF format (cp. Fig. 5.22 "Export PDF").
  
  Fig. 5.22: The situation analysis table (SAT) for a sample project.
- Edit Project
  
  This page allows you to modify the details for an existing project. You can easily update the project's name and description, select the groups that are responsible for the project (and will therefore be able to submit reports for it) and define the project's start and end date.
  
  Note that the project name and description, as well as its start date constitute mandatory information, while the definition of project heads and an end date is voluntary.
  
  Fig. 5.23: A screenshot from the project administration page.
- Modify the Structure of the Situation Analysis Table
  
  The situation analysis table (SAT) is meant to be a convenient way for all people involved in a large, on-going project to assess the current state of the project and to see which checkpoints have been reached already, which objectives have been achieved and which are still outstanding.
  
  The creator of a project can modify the layout of the SAT and define all objectives, deliverables and checkpoints for the project. Fig. 5.22 shows a sample SAT definition. Node how you can easily add or remove components from the SAT and change their order by dragging and dropping rows.
  
  Although, not strictly necessary, we would recommend that you define a due date for all checkpoints and objectives in the project, so StemDB can help you to monitor the progress of the project (cp. viewing the SAT).
  
  You can furthermore export a complete overview of the project to a printer-friendly PDF format (cp. Fig. 5.22 "Export PDF").
  
  Fig. 5.24: The situation analysis table (SAT) for a sample project.

[Return to Table of Contents]

Frequently Asked Questions (FAQ) [ToC]
- How do I obtain a StemDB User Account?
  
  To sign up for a user account click here. Registration is free of charge.
- Do I need a user account to submit data to StemDB?
  
  Yes, you will have to register with StemDB and log into your account in order to submit new entries to StemDB. This allows us (and you) to keep track of the ownership of records. Furthermore, only users that are members of certain, approved collaborations can submit data (cp. Collaborations).
  
  To sign up for a user account click here.
- Help! I forgot my password!
  
  There is no reason to worry. You can simply request a new password to be sent to the email address you specified when you registered with StemDB. Please follow this link to request a new password.
- Can I link to specific entries in StemDB?
  
  Yes, use the following URL and replace the accession number in it by the one of the entry you'd like to link to:
  http://www.stemdb.org/stemdb/utils/show?id=ACCESSION_NUMBER
- I am using StemDB to manage an international project, however, when I try to use a web conferencing software to display an SAT the page is not displayed correctly!
  
  The browser software integrated in this kind of tools is often very old and does not support the full range of modern browser's dynamic, rich features. We have created a simplified version of the project management interface for this purpose which is accessible under:
  http://www.stemdb.org/stemdb/marratech
- I have registered for a StemDB user account, but I can still not submit any data!
  
  Submission of data to StemDB has been restricted to members of certain, approved collaborations in order to ensure a consistent, high quality of all data. You can gain the right to submit data by joining one of the approved collaborations or by creating an own collaboration and obtaining deposit rights for it.
[Return to Table of Contents]
Appendix - Search Terms

The search engine uses the following field names for indexing StemDB Information, by datatype:
- Antibody
  
  name, clonality, target, raised_in, isotype, immunogen, concentration, specificity, species_reactivity, conjugation, company, catalogueno, applications, location, description, comments
- Cell Line
  
  name, celltype, strain, tissue_of_origin, type, germline_competency, derived_from, karyotype, sex, morphology, storage_location, culture_medium, subculture_routine, comments, species, trivial_name
- Document
  
  title, pubmedid, author, abstract, url, type, date, journal, description, document
- Gene Expression Experiment
  
  title, keywords, type, chip_type, goal, description, comments, parameter_value, sample_id, qc_report, report_type, comments, dbxref_external_id
- Primer
  
  name, five_primer_name, three_primer, five_primer, three_primer_conc, five_primer_conc, upl_probe_id, amplicon_size, opt_timperature, real_time_control, pcr_reagents, tested_for, comments, gene_target, species, trivial_name
- Protocol
  
  title, keywords, category, description, document
- Rodent Strain
  
  name, genetic_background, recombination_comments, genotype_procedure, phenotype, derived_from, comments, description, species, trivial_name
- Project Report
  
  consortium, abstract, publications, patents, other, lead_scientists, projectname, project_id, type, name, description, document
[Return to Table of Contents]

StemDB Manual

Table of Contents:

Introduction [ToC]

User Accounts, Groups and Collaborations [ToC]

Data Retrieval and Submission [ToC]

Project Management [ToC]

StemDB Functionality by Page [ToC]

Frequently Asked Questions (FAQ) [ToC]