{scrollbar:icons=false} |
This section introduces you to the procedures for searching the Biospecimen Research Database. It includes the following topics:
You can search the Biospecimen Research Database (BRD) to find research papers and studies that match criteria you specify. Each published paper is associated with one or more studies that address specific experimental questions. If you do not narrow your search by selecting search criteria, then all studies in the database will be returned as search results.
You can search the BRD in the following ways.
You do not need to log in or have an account to search the Biospecimen Research Database. |
From the BRD home page, all search options appear when you click the Search tab.
The home page also contains a News and Announcements section, a Featured Paper identified by a BRD Curator, and lists of papers that have been added recently as well as those that were recently viewed by you. A Twitter feed from the NCI Biospecimens account is also displayed. If you want to share information on the BRD, compose a new tweet via your personal Twitter account using the #BRD hashtag.
Located in the top right portion of the header on every BRD page, is a keyword search box labeled Search BRD Papers. You can search very quickly for any paper in the BRD by using any keyword including paper information, authors, free text, biospecimen location or type, or pre-analytical factor.
The Simple Search is highlighted in red in the screenshot below.
An Advanced Search includes all possible search criteria in a query format. This is the default search method. For more information, see Conducting an Advanced Search.
The Browse by Analyte search option displays the contents of the BRD in a table that is organized by both the analyte investigated and the biospecimen type and location used for analysis. The numbers within the table contain links to search results that correspond to the biospecimen type/location and analyte selected. From the Search Results page, you can toggle between results for other analytes for a given biospecimen type and location without the need to return to the Browse by Analyte page. For more information, see Browsing by Analyte.
The Browse by Pre-analytical Factor search option displays the contents of the BRD in a table that is organized by the experimental questions addressed (pre-analytical factor) and the biospecimen type/location used for analysis. Due to the large number of pre-analytical factors captured by the BRD, the table can be restricted by selecting a Classification or directly entering a pre-analytical factor. The number links in the table represent all of the relevant papers in the BRD for the corresponding pre-analytical factor listed in the row. For more information, see Conducting a Pre-analytical Factor Search.
You can conduct a Simple Search for a paper from any BRD page. Enter any keyword associated with the area of interest (such as a tissue type, diagnosis, biomarker, fixative, anticoagulant, and so on) or a specific paper (such as the PubMed ID, title, journal, year, and so on). N ote that gene symbol use within the BRD is not standardized and it is recommended that you search using the full gene name. Also, if you are searching for a specific author, use the Author(s) search option on the Advanced Search page. Specificity can be increased by including multiple words with or without search operators. If using multiple search operators, use parentheses to control query logic. Search operators that are supported by Simple Search, example queries, and their anticipated results are summarized in the table below.
Simple Search Operators | Example | Results |
---|---|---|
Double quotes (" ") will return curations that contain the exact phrase quoted. | "sodium heparin" | Curations containing the exact phrase sodium heparin |
Including AND or + between search phrases will return curations that contain both search phrases. If more than one search term is entered, this search operator will be applied as the default. | formalin AND paraffin or formalin + paraffin or formalin paraffin | Curations containing both formalin and paraffin |
Including OR between search phrases will return curations that contain either search term. | frozen OR fresh | Curations containing either frozen or fresh |
Including NOT or - (minus) between search terms will return curations that do not contain the term that follows the operator. This operator must be used with a search term that will return results. | immunohistochemistry NOT "tissue microarray" | Curations containing immunohistochemistry but not tissue microarray |
An asterisk (*) is a wild-card search operator that can replace any number of characters in a search term. It can be used in the beginning, middle or end of a search term. | freeze-thaw cycl* | Curations containing either freeze-thaw cycle, freeze-thaw cycles, or freeze-thaw cycling |
A question mark (?) is a wild-card search operator that replaces a single character in the search term. It can be used in the beginning, middle or end of a search term. Multiple question marks can also be used within a single search term. | K?EDTA | Curations containing the term K2EDTA or K3EDTA |
A tilde (~) is a search operator that will return terms that are spelled similarly to the term that prefaces it. It should follow a single word search term. | anesthesia~ | Curations containing the terms anesthesia, anaesthesia, or anesthetized |
Search operators can be used together and parentheses can be used to group queries. | circulating AND (microRNA OR miRNA) | Curations containing circulating and either microRNA or miRNA |
The proximity of two search terms to one another can be specified by placing the terms in quotations followed by a tilde (~) and the number of words allowable. | "circulating DNA"~2 | Curations containing circulating DNA, circulating cell free DNA or circulating cell-free DNA. |
Prefacing a search phrase with pubMedId: will limit the query for the search phrase to the PubMed ID field. | pubMedId: 24486652 | A single curation with the PubMed ID 24486652 |
Prefacing a search phrase with title: will limit the query for the search phrase to the Paper Title field. | title: hemoglobin | Curations that contain the word hemoglobin in the paper's title |
Prefacing a search phrase with publicationName: will limit the query for the search phrase to the Journal of publication field. | publicationName: Biopreserv Biobank | Curations that were published in the journal Biopreserv Biobank |
Prefacing a search phrase with curatorPurpose: will limit the query for the search phrase to the Purpose of Paper field. | curatorPurpose: "storage temperature" | Curations that contain the exact phrase storage temperature in the Purpose of Paper field. |
Prefacing a search phrase with curatorConclusion: will limit the query for the search phrase to the Conclusion of Paper field. | curatorConclusion: clinically relevant | Curations that contain the words clinically and relevant in the Conclusion of Paper field. |
Prefacing a search phrase with purpose: will limit the query for the search phrase to the Study Purpose field. | purpose: ischemia | Curations that contain ischemia in the Study Purpose field. |
Prefacing a search phrase with summaryOfFindings: will limit the query for the search phrase to the study's Summary of Findings field. | summaryOfFindings: statistically significant | Curations that contain the words statistically and significant in the Summary of Findings field. |
To conduct a Simple Search
An Advanced Search of the Biospecimen Research Database provides you with the most control over search criteria and results in comparison to other search options.
When specifying search criteria in the Biospecimen Research Database, 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).
If you don't specify any criteria, all entries in the BRD appear in the search results. |
If a paper you are looking for is not in the BRD, you can suggest a new paper. |
To conduct an Advanced Search
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 studies that concern both cells and kidneys.
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. |
The following table describes the Advanced Search criteria.
Advanced Search Criteria | Description | |
---|---|---|
Specimen |
| |
Biospecimen Type | Select the type of biospecimen (Tissue/Fluid/Cell). | |
Biospecimen Location | Select the bodily location from which the biospecimen was obtained. | |
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.
| |
Preservative Type | Select the substances added to the biospecimen, or other treatment to protect it from chemical change or microbial action. | |
Platform |
| |
Analyte | Select the analyte, or endpoint that was qualitatively or quantitatively examined in the biospecimen. Select "Morphology" for macro- and microscopic analysis. | |
Technology Platform | Select the specific technology used to analyze the biospecimen. | |
Author(s) | Enter the author’s name(s) in the format of last name followed by first initial (first initial is optional). Separate authors' names by a comma. Use " * " as wildcard. Examples: Smith J, Doe L
| |
Paper Type | Select among the paper type options: Review, Non-review, or All. If you do not select any search criteria prior to clicking the Search button, the search uses Paper Type: All as its default search criterion. | |
Pre-analytical Factors |
| |
Classification | The type of biospecimen handling variable that was the subject of the study (pre-acquisition, post-acquisition, or platform specific) | |
Factor | The specific pre-analytical factor that was the subject of the study (e.g., the post-acquisition variable, "type of fixative," is a specific pre-analytical factor in a study that examines the effects of different types of tissue fixatives on molecular analysis). |
If you want to search for items not present in the drop-down lists such as specific genes or biomarkers, enter those items in the Keyword box. Multiple words can be entered with or without a search operator to increase specificity. See Conduct a Simple Search for a list of supported search operators. This search method searches all fields including paper information, authors, summary fields, and Pre-analytical Factors and their values. The keyword search can be used together with other fields on the Advanced Search page.
Gene symbol use is not standardized, so search by the full gene name. |
On the search results page, you can:
Click the Study Purpose hyperlink to view detailed information about the study.
Paper and study details are both on the Paper Details page. Click View More or View Less to show or hide the study details. |
When you browse the BRD by analyte, you can navigate between analytes for a given biospecimen location by clicking a number link in the table.
If a paper you are looking for appears to be missing, first run an Advanced Search and then consider suggesting a new paper. |
To browse by analyte
Click Browse by Analyte, which is located under the Search tab. The Browse by Analyte page appears, displaying all of the papers in the BRD within a table that is organized by biospecimen type and location and analyte(s) investigated.
Click a number link as explained in the following table.
Click a link in the... | To see... | |
---|---|---|
Biospecimen columns | all research studies in the database that involve that biospecimen location or type | |
Analyte columns | all research studies in the database that involve that analyte | |
Body of the table | all research studies in the database that involve the unique combination of biospecimen location, biospecimen type, and analyte in that table row.
|
Studies that match of the criteria you selected appear in the table.
On the search results page, you can:
Click the Study Purpose hyperlink to view detailed information about the study.
Paper and study details are both on the Paper Details page. Click View More or View Less to show or hide the study details. |
Browsing by Pre-analytical Factor allows you to find research studies corresponding to selected Pre-analytical Factors.
If you are not able to find a specific paper, first run an Advanced Search and then consider suggesting a new paper. |
To browse by Pre-analytical Factor
Click a number link as explained in the following table.
Click a link in the... | To see... | |
---|---|---|
Pre-analytical Factor column | all research papers and studies in the database that involve that Pre-analytical Factor | |
Classification column | all research papers and studies in the database that involve that Classification | |
Body of the table | all research papers and studies in the database that involve a unique combination of Pre-analytical Factor, Classification, and either bodily fluid or cells/tissue in that table row. The numerical link corresponds to the number of papers that fulfill the search criteria combination.
|
Studies that match of the criteria you selected appear. Note that your search criteria appear above the list of papers and studies.
On the search results page, you can:
Click the Study Purpose hyperlink to view detailed information about the study.
Paper and study details are both on the Paper Details page. Click View More or View Less to show or hide the study details. |
Once you have searched the database and are viewing your results, click the paper title to open the Paper Details page, where you can view a paper’s entire record. Click the Study Purpose and open the Paper Details page at the section for that study's details.
Each paper includes one or more associated studies. Studies are defined as the set(s) of experiments within a paper that investigate different pre-analytical factors, use different analytical platforms for analysis, or explore different biospecimen sample sets. For example, a paper that examines the effect of a biospecimen handling variable on RNA and protein analysis may have two studies in the database, one study describing the results of RNA analysis and one describing the results of protein mass spectroscopy analysis.
On the Paper Details page, you can:
You can also choose to expand the page to view all of the study details, including:
You can search the BRD for related studies with the same biospecimen type and location, classification(s), and pre-analytical factor(s) by clicking the links in the study details.
To return to your search results, click most recent search results... at the top of the page.
Add a comment to a paper to share your thoughts with others using the BRD. 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 paper
To sort the comments, select one of the following options from the Sort by list:
To share the comment, click Share and then click either the Twitter or the Facebook icon.
To make the paper a favorite, click the star icon next to Favorite.
For more information about using Disqus, see the Disqus Knowledge Base.
If you know of a paper that would be a useful addition to the Biospecimen Research Database, you can suggest it. Paper suggestions are screened against BRD contents to prevent duplication. Curators will review each suggestion and add BRD-appropriate papers to the database.
If you include your email address you will receive an update when your paper suggestion has been added.
To suggest a new paper
{scrollbar:icons=false} |