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CHTN's Transient Inventory Data Access Launchpad (TIDAL)
Transient Inventory Data Access Launchpad (TIDAL) is an application at the Cooperative Human Tissue Network Eastern Division (CHTN-ED). The CHTN is a prospective procurement service organization. It assists the scientific community in obtaining biosamples for research and advancing scientiftic research and knowledge. Even though all projects utilizing CHTN service must be prospective in nature (See Prospective Procurement vs. Biobanking below), all CHTN divisions have transient inventory on hand. Transient Inventory are those biosamples that were collected but may not have satified use-case for a variety of reasons. These are still high-quality, histopatholically reviewed biosamples. The CHTN 'Banks' these biosamples for future use. This application allows CHTN Investigators to conduct searches on transient inventories held at certain CHTN locations through TIDAL's federate database model. To receive biosamples from the CHTN you must have an active, accepted protocol with a CHTN division. If you are not a CHTN Investigator, you can apply to the CHTN by downloading the application here or by contacting the CHTN Eastern Divison (215) 662-4570.

After conducting a TIDAL search, you can request biosample(s) in which you are interested (You must have an active protocol and the biosamples must be verified for use before receipt).

We've put answers to commonly asked questions and a How-to-user-guide on this page. You can either read down the page or click items of interest in the table of content (TOC) to the left.

What is CHTN?
The Cooperative Human Tissue Network (CHTN) is a National Cancer Institute supported organization of five academic and one pediatric institution. Its core mission is to supply prospectively procured human biosamples to the research community (Links to the six divisions can be found in the footer). The six divisions are: Eastern at the University of Pennsylvania Perelman School of Medicine; Mid-Atlantic at the University of Virigina; Mid-Western at The Ohio State University; Southern at Duke University; Western at Vanderbilt University; and, the Pediatric Division is at Nationwide Children's Hospital. The central CHTN website can be found here.
Prospective Procurement vs. Biobanking
The CHTN is NOT a traditional biobank resource. All services utilizing the CHTN must be conducted under an approved prospective procurement model service. This means that a researcher (investigator) makes an application to the CHTN outlining a collection protocol. The CHTN monitors activities at several sites looking for biosamples. When a biosample is available for collection and matches an investigator's protocol, that biosample is collected, reviewed for histopathologic quality (percentage of material, designation of annotation, etc) and analyzed with regard to the requesting protocol. If passed both Histopatholoic quality and request protocol reviews pass, the biosample will be distributed to the investigator.

Through the years, some samples were collected that are high quality but did not match the requesting investigator's outlined protocol. In this case, the CHTN division holds the biosample within inventory, esentially 'banking' the biosample (Transient Inventory). Each division can utilize this inventory to fill other requests or future requests made by the research community. Even though all projects utilizing the CHTN must be prospective procurement in nature, all CHTN divisions have transient inventory on hand. The CHTN is NOT a banking organization and attempt to not hold inventory. To receive biosamples from the Transient Inventory, an investigator still must have a valid and active request protocol within the CHTN systems.

So What is TIDAL?
This tool allows the research community to conduct searches on the transient inventories held at various participating CHTN locations through the CHTN's federated database. A federated database is defined by: a service in which data is controlled at the individual division; a query is made from a central location and each participating service decides how best to answer the query; Each participating service returns a recordset to answer the query. In this way, participating organization do not need to supply data to a centralized dataserver. Rather a query request is made to what is called a public accessible data webservice. The webservice fulfills the query through a 'contact' with the TIDAL application. The TIDAL application makes the query request of the various services and then conglomerates the data for display. In this way, TIDAL offers current views of Transient Inventory held at the various divisions. To receive biosamples from the CHTN you must have an active, accepted protocol with a CHTN division.
The Criteria Page - Keep it simple
TIDAL attempts to keep search request simple. The criteria page reflects this - There are only four data elements listed on the page: 1) Specimen Category; 2) Site (organ/primary/anatomic), this can include sub-site designations; 3) Diagnosis (condition/designation/modifications); 4) Preparation Specification. To learn more about these data elements and their uses, either scroll down or click on a hyper-link within the list.

The specimen cateogry and preparation fields are the only parameterized fields, the other two fields are free-type. This allows for entry of any term that may be desired (even though CHTN has a vocabulary that is used for annotations, some biosamples are pulled from other sources and may not use this standardized vocabulary. A user is encouraged to review the CHTN vocabulary in the 'Ontologic vocabulary suggestion' tool. However, because of the different ways of annotation, users are also encouraged to perform their own word-choice searches.

There is a 'Captcha' code security feature on this page. This allows the research community at large to perform these searches without having to create accounts within the app for security. Typing the code that is shown will commit the search (this allows the TIDAL app to discredit requests from 'web-bots'). If the code is hard to read or otherwise needs to be refreshed, there is a 'New Captcha Code' button to refresh the code.

NOTE: On the criteria screen, all field labels are 'click-able' to bring the user to this documentation page.

When a user has finished inputing the required parameters of the request to be queried, the user clicks the 'Submit' button near the bottom of the input screen.

Using the 'Specimen Category' Search Field
Specimen Category (also refered to as Tissue Type) is an overarching term within the diagnosis designation ontology to outline a braod diagnosis condition. This is NOT a required field but would assist in limiting results more braodly. For instance, perhaps the user is looking for cancerous conditions in the thyroid - such as carcinomas and adenocarcinoma. Instead of doing two searches (Thyroid - Carcinoma / Thyroid - Adenocarcinoma ), the user could choose: Malignant / Thyroid, which would limit the results to 'Malignant' subtypes of diagnosis with a site of thyroid. To search specifically for Carcinoma within thyroid, the designation of malignant is NOT required.

This is a parameterized field, meaning that only those values that are in the standard CHTN vocabulary appear on this list. Only one value at a time can be choosen. If more than one condition needs to be limited by this field, more than one search will need to be performed.

Using the 'Site (Organ/Anatomic)' Search Field
To perform a search, there are only two required elements - Preparation (discussed below) and a co-joined requirement of either Site or Diagnosis (Diagnosis is discussed below). The Site criteria field is labeled 'Site (Organ/Anatomic)'. In this field the user can specify any organ/anatomic site for which they are searching. This includes, sub-sites with common vocabularies. For instance, a user could specify 'Thyroid', which would return all biosamples with the designation of a thyroid - including all the thyroid's subsites (ISTHMUS | LOBE | PYRAMIDAL). However, in this field the user could also specify 'Pyramidal' which would retreive any biosamples that are annotated with that designation. Be aware, that not biosamples are annotated to that level and not all webservice contacts may search a sub-site system with their vocabulary architectures. This concept is merely mentioned here as an option wihtin the search dictum. Some CHTN web-services contracts perform exact matching - some perform a 'like' match. In database science, a like match can be performed to find conditions within the beginning / middle / end of terms. Entering a short term will broaden the search results, entering a longer term will restrict the results.
Using the 'Diagnosis' Search Field
To perform a search, there are only two required elements - Preparation (discussed below) and a co-joined requirement of either Site or Diagnosis ('Site' is discussed above). The diagnosis site is labeled 'Diagnosis'. In this field the user can specify any diagnosis condition. For a list of possible values, the user can the TIDAL's 'List of Vocabulary Suggestion' tool. However, the suggestion tool does not provide all possible values. This field can include all modifier of a diagnosis condition. For instance, searching Carcinoma will also display modifier of Adenocarcinoma - but searching Adenocarcinoma will NOT retrieve all possible other carcinomas. Some CHTN web-services contracts perform exact matching - some perform a 'like' match. In database science, a like match can be performed to find conditions within the beginning / middle / end of terms. Entering a short term will broaden the search results, entering a longer term will restrict the results.
Selecting 'Preparations'
The 'Preparation' options are pre-defined methods of preparing a biosample for storage. Within each option there many be many deliniations - such as a preparation of 'Slide' would contain methods of 'H&E' (Haematoxylin and Eosin Stained slides), Unstained Slides, Supplied Stains, etc. Additionally, deliniations of preparation are found under differing preparations. Some institutions classify Paraffin Embedded Block as preparation of 'FIXED' where other institutions seperate 'FIXED' biosamples as distinct from 'Paraffin Block'. Users will find Formalyn-Fixed Paraffin Embedded (FFPE) blocks under both a preparation of 'FIXED', as well as 'PB' (for paraffin block). When performing searches for with a particular preparation in mind, a user should be cognizant of these facts.

When constructing queries, a user is not limited to a single preparation type. This is a multi-select option field.

Listing Ontologic Vocabulary Suggestions

As an effort to assist in searching the transient inventory, TIDAL offers a Ontologic Vocabulary search tool. This tool displays vocabulary used to annotate biosamples within the CHTN. Again, these are merely suggestion of search terms - as there are other source of biosamples besides the CHTN that supply varied annotations. When first opening this screen, the user is presented with a site list displayed on the left hand side. This list is scrollable and in alphabetical order. In addition to displaying the site, this list also lists any sub-sites that would be included in the search parameter for this term - example: under the term 'Thyroid', the terms 'ISTHMUS | LOBE | PYRAMIDAL' are listed as subsites. Clicking on a term on the left will open up the diagnostic term list for that site on the right side of the screen. This term list is organized by 'Specimen Category'.

NOTE: To reiterate, these are merely suggestions from the 'official approved' vocabulary of the CHTN. Biosamples may have been annotated at different institutions and added to the transient inventory - or the vocabulary used by the CHTN division was an 'override' value. This function within TIDAL is merely as a suggestive function or a browser of what may be possible.

Note:

Displaying the Results of the Search
After the user has clicked the 'Submit' button on the query parameter screen, the results screen will be presented. The result screen begins with the progress interface (displayed to the right as image: Query Builder). This query build shows the progress of TIDAL sending and receiving data from disperate data services within the federated database. Depending on the speed of the internet connection, thenumber of webservices being queried and the number of biosamples being returned by those services, this process could take as long as one minute. Once the process is finished the resultant recordset will be displayed.

 


Once the Query build is finished with its processing, a grid display is presented to the user showing a recordset of results (image above: Resultant Recordset). The menu bar across the top of the screen has changed from navigational focus to a data function focus. The functions on the menu bar are as follows:
1) New Search: This function will take the user back to the basic query parameter screen. In this release, TIDAL does not save query parameters for re-query. So navigating back to the query screen creates a new query object within the TIDAL database.
2) Select All/Select None: To request biosamples from the CHTN/TIDAL service the user needs to indicate interest in selected biosamples. The user either selects individual biosamples by clicking on the biosample data row (more on this below), or the user can click the 'Select All' function menuitem. This will select all biosamples in a recordset. When the user clicks this menuitem, all biosamples will be selected and the menu item will toggle to read 'Select None'. The menuitem will now de-select all biosamples in the recordset.
3) Request Selected: Once the user has selected at least one biosample, clicking the 'Request Selected' will package the selected biosamples into a data stream to send to the various CHTN divisions. This will also display a contact form to fill out to request those selected biosamples - for more information about sending the request, see Requesting Biosamples below.
4/5) Export All/Export Selected: The next two menu items perform the same basic action. If the user wishes to copy the data to a local PC for analysis, the export function will package recordset into a CSV (comma-seperated value) delimited file and will download to the local PC. When the user selects this option, the local PC will alert the user to save the file or open it. If the local PC is setup to recognize CSV as delimited to Microsoft Excel (or another spreadsheet application - such as open-office or libre office), the file can be opened in those applications. The difference between Export All/Export Selected - Export Selected will export only those biosample that have been selected on the result recordset.
6) Display Paratmers: This menuitem will display a 'pop-up' showing the query parameters used to generate this recordset.
7) Biosamples Found: This menuitem is a display function only. This menuitem displays how many biosamples are in the recordset. When the user selects biosamples from the recordset, this menuitem will change to show a ratio of how many selected to how many exist.

One of the nice things about TIDAL is that when a user creates a parameterized search, that search creates a data object with a unique ID in the TIDAL database. This can be seen in the URL of the browsers address bar. By bookmarking this URL, the user can run the search again and again looking for new and interesting biosamples without having to re-input criteria selections - or the URL can be copied and email to a collaborator to share data.

The Result Grid Column Abbreviations

The recordset is defined by individual biosamples in rows down the page. Those biosamples data element annoations are in columns. If there is a sort icon in the header square, the icon is clickable to sort that column. Within this release of TIDAL, only one column at a time is sort-able.

The data elements represented within the recordset are as follows:
1) The first column is un-labled. This column contains a 'page' icon is the biosample has a displayable pathology report. Clicking this 'page' icon next to the biosample will open the pathology report for the user's review. Depending on the source of the biosample some pathology reports will open in seperate browser tabs and some will open in the same window.
2) Label: This column contains the CHTN Division's identification label for this biosample - some organizations refer to this as the label number - some CHTN Divisions refer to this number as the CHTN number. This is a sortable column.
3) Category is the specimen category (some times refer to as Tissue Type) is the over-arching designation for the annotated diagnosis of the biosample. This is a sortable column.
4) Site is the anatomic/organ/tissue site of the biosample. This column will include any sub-sites annotated within the site designation of the biosample. This is a sortable column.
5) if applicable, Primary Site is the primary site of any tumor condition. This can also be refer to as 'metastatic from site'. This will only include data for annotated diagnostic malignant cases. This is a sortable column.
6) Diagnosis / Diagnosis Modifier is the column containing the data annotation of disease condition. This is a sortable column.
7) Biosample Preparation is the data denoting the preparation and under lying preparation method of the biosample. This is a sortable column.
8) Size Metric: The size of the biosample - either a weight metric (usually in grams) or size metric (widthxlengthxheight) - some biosamples do not contain a metric - such as slides. This is NOT a sortable column
9) Procedure: indicates the type of transaction the biosample was retreived from the donor. The two most common procedure types are Surgery and Autopsy - however, there many be a number of others, like biopsy, phlembotomy, etc. This is NOT a sortable column.
10) Hour Post - the column name here is abbreviated for hours post excision or hours post autopsy. It represents the time to the closest 15 minute estimate by the procuring technician of time until fixation - this is an estimate by CHTN technical procurement technicians.
11) Age/Race/Sex: the biosample donor's age at time of procurement / race and genetic sex. Some CHTN divisions track Sexual orientation and gender identity annotation data points. Contact the individual division for more information outside of genetic sex.
12) Cx/Rx - This columns stands for Chemotherapy and radiation treatment history of the donor pre-procurement. For more information on treatment specifics, contact the procuring division (note, dependent on biosample this could result in a CHTN chart review charge).

One of the nice things about TIDAL is that when a user creates a parameterized search, that search creates a data object with a unique ID in the TIDAL database. This can be seen in the URL of the browsers address bar. By bookmarking this URL, the user can run the search again and again looking for new and interesting biosamples without having to re-input criteria selections - or the URL can be copied and email to a collaborator to share data.

Selecting biosamples of Interest
To select a biosample of interest, click on the recordset biosample row on the result grid or click the 'Select All' menu item.
Sending a Request for Biosamples
After a user has selected one or more biosamples of interest, the user click the 'Request Selected' menu item at the top of the page. This action will open the 'Request Biosamples' form (see image to left 'Sending a request'). On this form fill out your contact information: name, phone, email and if you are a CHTN investigator your CHTN Investigators ID. Input the code in that is displayed in the captcha field. Once finished, click the 'Send' button. This will package the selected biosamples together and email your information along with your request to the responsible CHTN divisions holding those biosamples (You will also receive a copy of the email to the email address which you supplied.