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This section introduces you to the procedures for searching, viewing, and downloading Standard Operating Procedures (SOPs) and SOP Compendiums in the Biospecimen Research Database (BRD). It includes the following topics:

Overview of Standard Operating Procedures

An SOP provides instructions for a process for which uniformity in performance are optimal and sometimes required. In BRD, SOP types are organized hierarchically, with progression to a higher level representing the work invested and the confidence the Biorepositories and Biospecimen Research Branch (BBRB) has in the document. From lowest to highest, SOPs progress through the following levels: SOP, Biospecimen Evidence-Based Practices, and Expert-vetted.

SOPs are version-controlled. Each time a new version is available in the BRD, the SOP receives a new unique identifier, called a BRD ID, allowing you to clearly identify differences between SOPs that may have clinical and scientific implications.

SOPs are available to the public. To provide comments on specific SOP versions, register with Disqus or log in with your Facebook, Twitter, or Google account. All comments are subject to moderation by the BRD Curation Team.

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Searching for an SOP

You can search for SOPs by keyword or by selecting a curated field.

When searching for an SOP, there are no required fields. You can add as much detail or only those criteria that you consider essential to the search. You can also select multiple search terms in the same list by selecting the first item, pressing and holding Ctrl, and then selecting the next item(s).

To search for SOPs

1. Select Search > Search SOPs.
   The Search SOPs page appears.
   
2. For maximum search accuracy, specify search criteria by clicking items in the lists.
   
   • To select multiple fields in the same list, click the first field, press and hold the CTRL key, and then click additional fields. The fields you select are highlighted and your search results contain all SOPs matching any of the fields. For example, if you select both the Cell and Fluid biospecimen types, your search results contain all SOPs that concern either cells or fluid.

   • When you select fields from different lists, you narrow your search. For example, if you select the Cell biospecimen type and the Kidney biospecimen location, your search results include SOPs  that concern both cells and kidneys.

     The following table describes the SOP search criteria.

     Note that the selections you make in the lists on the left determine the selections in the lists on the right. For example, selecting the Biospecimen Type “Fluid” makes “Blood” an available Biospecimen Location.

     SOP Search Criteria	Description
     Source	Select the organization or institution that developed the SOP.
     Tier	SOPs are organized in a hierarchy system. The base tier is SOP. Progression to a higher tier will represent the work invested and the confidence level BBRB has in the document. SOP: A library of collection of SOPs reviewed and formatted for public dispersal. Biospecimen Evidence-Based Practices: An SOP that has been transformed into evidence-based procedural guidelines. The protocols are more flexible, indicating the optimal but also acceptable practices when possible. Evidence is summarized in "Summaries of Literature Evidence" and includes internal citation and two reference sections (one for laboratory guidelines and one for literature references). Expert-vetted: After a Biospecimen Evidence-Based Practice served as the topic of a expert workshop, feedback from the workshop would be applied to the document.
     Specimens
     Biospecimen Type	Select the type of biospecimen (Cell/Fluid/Tissue).
     Biospecimen Location	Select the anatomical location from which the biospecimen was obtained.
     Diagnoses
     Diagnosis	Select the term that identifies the nature of a disease or condition associated with the biospecimen.
     Diagnosis Subcategory	Select the diagnosis subdivision that differentiates the disease within the larger category. Diagnosis Subcategory is only available for the diagnosis "neoplastic.”
     Topics
     Topic	Select the topic or scope of the SOP document.

3. If you want to search for items not present in the lists such as specific genes or biomarkers, enter those items in the Keyword(s) box. A keyword search searches all curated fields as well as the SOP document.To increase specificity, you can combine the keyword search with other fields on the Search SOPs page. You can enter multiple words into the Keyword(s) box with or without a search operator. See Conduct a Simple Search for a list of supported search operators. See the table below for field-specific search operators.

   All fields and search operators are case-sensitive.

   Field-Specific Search Operator	Example	Results
   Prefacing a search phrase with Title limits the query for the search phrase to the SOP title.	title: GTEx	All SOPs containing the word GTEx in their title fields.
   Prefacing a search phrase with Description limits the query for the search phrase to the SOP description.	description: "surgical tissue"	All SOPs containing the exact phrase "surgical tissue" in their description fields.
   Prefacing a search phrase with BRD-ID limits the query for the search phrase to the BRD ID.	brdId: 8	The single SOP with a BRD ID of 8.
   Prefacing a search phrase with Body limits the query for the search phrase to the SOP document.	body: procurement procedure	All SOPs containing the words procurement and procedure in the body of the document.

   Gene symbol use is not standardized, so search by the full gene name.

4. Click Search.
   The Search SOPs Results page appears, summarizing your search criteria and the SOPs matching them. Click any SOP title to view the SOP.
   

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Viewing and Downloading SOPs

Clicking an SOP on the Search SOPs Results page opens the SOP page, where you can view a detailed description of the SOP and download associated SOP files.

When multiple SOP versions exist for a single SOP, you can download them as a ZIP file.

To view an SOP

1. Search for SOPs.
   The Search SOPs Results page appears.

2. Click an SOP title link.
   The SOP page appears.
   

   Return to the search results by clicking most recent search results... (A) at the top-left of the page.

3. Note the following information about the SOP on this page:
   • The BRD ID is unique for this version of the SOP.
   • You can add the SOP to a session compendium (B).
   • You can select a different version of this SOP from the Version (Release Date) list (C).
   • The source of the SOP is listed.
   • The tier (SOP, Biospecimen Evidence-Based Practices, or Expert-vetted) of this SOP is listed. The SOP can progress to a higher tier.
   • A description of the SOP is listed.
   • Biospecimen types and locations, diagnoses, diagnosis subcategories, and topics represented in the SOP are listed.
4. Download the documents associated with this SOP by clicking links under Documents for Download (D. Files listed here are either in Adobe Acrobat or Microsoft Word format.
   
   • If more than one version of an SOP exists, click Download SOP documents of all versions instead to download a ZIP file of all SOP documents.
   • If the SOP is part of a larger compendium or family of SOPs, click the links under Associated SOP Compendiums (E). If the SOP is not associated with a compendium, this section does not appear.
   • If the SOP is related to another SOP of a higher or lower tier, click the links under Additional Tiers of this SOP. For example, if an SOP were promoted to the Biospecimen Evidence-Based Practices tier, creating a new SOP, the relationship between the two SOPs would appear in this section. If the SOP does not have a relationship to another SOP, this section does not appear.
     

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Commenting on an SOP

Add a comment to an SOP version to share your thoughts with others. Before you can comment, you must either register with Disqus or log in with your Facebook, Twitter, or Google account. All comments are subject to moderation by the BRD Curation Team. 

To add a comment to an SOP

1. On an SOP page, select the version of the SOP to which you want to add your comment.
   
2. Scroll to the bottom of the page to the comment box.
    
   Click the arrow next to Login and select the method by which you would like to log in: Disqus, Facebook, Twitter, or Google.
   
3. Follow the prompts to either create and log in with a Disqus account, log in with an existing Disqus account, or log in with a social media account. If you choose a social media account, you merge that account with Disqus and can log in with those credentials each time you want to comment. 
4. In the comment box, enter your comment. If you have not yet logged in, the application prompts you to log in using one of the methods in the previous step.
5. Click Post to complete the comment.
6. Optionally, sort the comments, share them on social media, and make the SOP a favorite.
   To sort the comments, select one of the following options from the Sort by list:

1. • Best - Comments with the most votes trending over time.
   • Newest - Most recent comments first.
   • Oldest - Oldest comments first.

To share the comment, click Share and then click either the Twitter or the Facebook icon.
 
To make the SOP a favorite, click the star next to Favorite.

For more information about using Disqus, see the Disqus Knowledge Base.   

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Understanding Versioning

Any time the BRD curation team updates an SOP or a compendium, a new version of that SOP or compendium is created with a unique BRD-ID. The most recent versions of the SOP or compendium are displayed by default. Differences may exist between versions that have clinical and scientific implications.

Before you download an SOP or a compendium, confirm that you have selected the correct version, if applicable. Versions are associated with a release date.

The following is an SOP version list:

The following is a compendium version list:

When multiple versions of an SOP exist, you can download all of them at once as a ZIP file. You can also download all SOP documents associated with a compendium at once as a ZIP file.

To download SOP documents of all versions

1. Search for an SOP.
   Search results appear. If multiple versions of the SOP exist, the SOP listing includes a Previous Versions field.
   
2. Select the SOP.
   The SOP details page appears.
   

   

3. Click Download SOP documents of all versions.
   Your browser prompts you to open or save a compressed folder of the SOP documents.
   
4. Open or save the folder.
   
   

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Overview of Compendiums

You can work with SOPs individually or with a compendium. A compendium is a family of SOPs that a curator has created. Compendiums can be project-specific.

You can also create a session compendium that lasts only for a work session. You can add any version of one or more SOPs to this compendium and then download them all at once as a ZIP file.

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Adding an SOP to a Session Compendium

DRAFT

To add an SOP to a session compendium

1. Search for an SOP.
   Search results appear. If multiple versions of the SOP exist, the SOP listing includes a Previous Versions field.
   

2. Click the + button next to the SOP title.

   You can also add an SOP to a compendium from the SOP page. Click the SOP title in the search results to open the SOP page. Click the + button next to the SOP title.

   The SOP is added to the session compendium.

3. To view all SOPs in the session compendium, click the folder icon next to the Help link at the top left of the page.
   
   
   

-How to add a SOP to the session compendium: there is a [+] next to the SOP title on the Search Results page and also the SOP page.  If a user clicks the [+] then the SOP is added to the Session Compendium.  The [+] changes to a [-], indicating that the user can then click on the [-] to remove the SOP from the Session Compendium.

-the additions are version-specific, meaning that a user can add a specific SOP version, and can add more than one version to the Session Compendium

Viewing Session Compendiums

DRAFT

Any user can create their own compendium that lasts only for the duration of a work session.

To view all session compendiums

• On the BRD home page, click the folder icon to the right of the ? help link.
  
  The My SOP Compendium page appears, listing all of the temporary compendiums in use in this session.
  

-To view the contents of the session compendium: Click on the folder icon to view the contents of the Session Compendium. The contents are displayed in a table.  Users can also remove SOPs from the Session Compendium using the Action column in the table. Users can download all SOP documents by clicking on the [Download all SOP documents] link.  Users can remove all contents in the Session Compendium by clicking the [Clear] link.

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Viewing Session Compendium Details

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Viewing All Compendiums

You can view all public compendiums and sort the list by title and release date.

To view a list of compendiums

• Select Search > SOP Compendiums.
  The SOP Compendium page appears, listing all public compendiums.
  
  
  You can do the following on this page:

• • Sort the list by title or release date by clicking the respective column heading.
  • Click an SOP title link to see the details for the SOP on the SOP page.

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Viewing Compendium Details

You can view the details of a compendium including its available versions and a list of all SOPs associated with it.

To view compendium details

1. Open the SOP Compendiums page.
2. Click a compendium in the list.
   The SOP Compendium page appears.
    
   
   You can do the following on this page:

• • Like SOPs, compendiums can have different versions. Select the version of the compendium (A) you want to view. 
  • The SOP section lists all of the SOPs included in this compendium. Select the SOP version and then click an SOP title (B) to view the SOP details page.
  • Download all SOP documents of the compendium version you selected (C).
  • Comment on this version of this compendium (D).

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Commenting on a Compendium

Add a comment to a compendium version to share your thoughts with others. Before you can comment, you must either register with Disqus or log in with your Facebook, Twitter, or Google account. All comments are subject to moderation by the BRD Curation Team.

To add a comment to a compendium

1.   Open an SOP Compendium page.
2. Select the version of the compendium to which you want to add your comment.
   
3. Scroll to the bottom of the page to the comment box.
    
   Click the arrow next to Login and select the method by which you would like to log in: Disqus, Facebook, Twitter, or Google.
   
4. Follow the prompts to either create and log in with a Disqus account, log in with an existing Disqus account, or log in with a social media account. If you choose a social media account, you merge that account with Disqus and can log in with those credentials each time you want to comment.  
5. In the comment box, enter your comment. If you have not yet logged in, the application prompts you to log in using one of the methods in the previous step.
6. Click Post to complete the comment.
7. Optionally, sort the comments, share them on social media, and make the compendium a favorite.
   To sort the comments, select one of the following options from the Sort by list:

• • Best - Comments with the most votes trending over time.
  • Newest - Most recent comments first.
  • Oldest - Oldest comments first.

To share the comment, click Share and then click either the Twitter or the Facebook icon.
 
To make the compendium a favorite, click the star next to Favorite.

For more information about using Disqus, see the Disqus Knowledge Base.     

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Suggesting a New SOP

If you know of an SOP that would be a useful addition to the Biospecimen Research Database, you can suggest it. SOP suggestions are screened against BRD contents to prevent duplication. Curators will review each suggestion and add BRD-appropriate SOPs to the database.

If you include your email address, you will receive an update once a curator considers your suggestion.

To suggest a new SOP

1. Click the Suggest a New SOP tab. The Suggest a New SOP page appears.
   
   
2. Enter the following required fields about yourself: name, email address, and organization.
3. Optionally, provide your phone number.
4. Enter the SOP's title.
5. Optionally, enter the SOP's version and description.
6. Click Browse to upload the SOP document.
7. From the Source list, select the organization or institution that developed the SOP.
8. In the Note to Curator box, indicate whether this SOP is part of a new or an existing Compendium. If this SOP is a new version of an existing entry, include any updates to fields here or specify them by selecting additional biospecimens, diagnoses, and topics (see steps 10-12).
9. Optionally, enter the BRD ID. This is the BRD ID of the last published version of this SOP, if applicable.
10. Select the biospecimen associated with this SOP suggestion, as follows:
    1. From the Biospecimen Type list, select a biospecimen. Options are Cell, Fluid, and Tissue.

    2. Select the anatomical location from which the biospecimen was obtained. 

    3. Click Add Biospecimen.

       You can add multiple biospecimen types and locations to the SOP suggestion.

11. From the Diagnosis list, select the term that identifies the nature of a disease or condition associated with the biospecimen, then click Add Diagnosis. You can add multiple diagnoses to the SOP suggestion.

12. From the Topic list, select the topic or scope of the SOP suggestion, then click Add Topic. You can add multiple topics to the SOP suggestion.
13. In the Verification area, enter the characters exactly as you see them. If you cannot see the characters you can click the refresh icon to obtain a new set of characters.
14. Click Suggest.

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