Introduction

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) [The TOC does not appear in the mobile version ot the application].

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 vs. Traditional 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.

Watch the Instruction Video *

* This video is embed through Youtube and may be blocked by some institutional firewalls. If so, just watch it when you are a more open network

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.

Conducting a Search

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.

Reviewing Data

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Selecting Records

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Sending a Request for Biosamples

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