Learn about the TIES system

TIES stands for Text Information Extraction System. It provides tools for de-identification and automated coding of free-text structured pathology reports. It also has a client that can be used to search these coded reports. The client also supports Tissue Banking and Honest Broker operations.

TIES focuses on two important challenges of bioinformatics:

  • Information extraction (IE) from free text
  • Access to tissue.

Regarding the first challenge, information from free-text pathology documents represents a vital and often underutilized source of data for cancer researchers. Typically, extracting useful data from these documents is a slow and laborious manual process requiring significant domain expertise. Application of automated methods for IE provides a method for radically increasing the speed and scope with which this data can be accessed.
Regarding the second challenge, there is a pressing need in the cancer research community to gain access to tissue specific to certain experimental criteria. Presently, there are vast quantities of frozen tissue and paraffin embedded tissue throughout the country, due to lack of annotation or lack of access to annotation these tissues are often unavailable to individual researchers.
TIES has three goals designed to solve these problems:

  1. Extract coded information from free text Surgical Pathology Reports (SPRs), using controlled terminologies.
  2. Provide researchers with the ability to query, browse and request annotated tissue data and physical material across a network of federated sources.
  3. Pioneer research for distributed text information extraction.

TIES provides the functionality required for:

  • organizations to de-identify and concept code a corpus of free-text SPRs and to create a data service which manages this information
  • organizations to provide role-based access to TIES data
  • authorized users to create queries of the TIES datastores and retrieve reports that fit these criteria
  • authorized users to submit requests for tissue (orders) which will be filled by Honest Brokers.

An important aspect of the interface is the ability to manage queries and case sets. Users are able to vet query results and save them to case sets which can then be edited at a later time. These can be submitted as tissue orders or used to derive data extracts. Queries can also be saved, and modified at a later time.

Potential Users

Some examples of potential TIES users are:

  • Attending physicians
  • Fellows
  • Department of Pathology Residents
  • Translational researchers
  • Oncologists
  • Basic scientists
  • Epidemiologists
  • Molecular biologists
  • Tissue Bank Personnel

System Architecture

TIES is designed as a three tier client-server architecture that is primarily written in Java. The user interface is implemented in Java Swing and deployed using Java Webstart. The middle-tier consists of OGSA-DAI based encrypted web services, and data processing pipelines. The NLP pipeline is implemented in GATE –  General Architecture for Text Engineering. It uses an Apache Lucene Index for search.

At the core of the TIES system are the identified(PHI data) and de-identified databases, and corresponding web-services that are used to access these databases. A typical TIES installation is spread over at least two different server machines, one each to hold the identified and de-identified data. The server holding the identified data and corresponding web service is behind the organization’s firewall and is not accessible from outside the organization. The server holding the de-identified data and its corresponding web-services is outside the firewall, enabling users to access TIES from outside the organization, and for the organization’s TIES node to share its data with other TIES nodes.

TIES uses MySQL as the DBMS, and since MySQL is network accessible, it is possible to store the databases on entirely different servers than the web-services for additional security. It is also possible to install TIES on just one machine.
TIES nodes must be part of a TIES network. The TIES network is managed by the CTRM. In the simplest scenario, a standalone TIES node is part of a single node CTRM. When nodes want to share data with other TIES nodes, they must share a common CTRM.

Data Model

TIES v5.5 Data Model. Click on the image to enlarge.datamodelxlargetrans


Data Processing

Reports undergo several stages of processing in TIES in order to be ready for search and retrieval by the users. Each stage is handled by a separate data processing service. Each report has a specific status field in the database that indicates the stage of processing.


Data Processing Stages

Data Processing Stages

male enhancement products iso test testosterone booster rhino male enhancement pills natural alternatives to viagra how to get an instant boner te best male enhancement pills testosterone booster free trial over the counter supplements for low testosterone cialis warnings wicked sex pills how to increase her sex drive best potency pills pills to last longer in bed over the counter vitality male enhancement permanent penis enlargement surgery is sildenafil as effective as viagra does weed increase libido legit male enhancement male enhancement rite aid best rated male enhancement pump penis enlargement natural sex stimulants birth control pills and low libido boost ultimate male enhancement review very low libido male what meds cause erectile dysfunction penis enhacement pills how to treat low libido in men orgasm medication sex spray side effects what is in gas station male enhancement pills buy viagra usa rse7en male sexual enhancement pill sex enhancement herbs company in china what male enhancement pill makes you hard penis pills top usa made all natural male enhancement pill uses for viagra other than ed names of penis enlargement pills list buy viagra india penis pills for big red bull male enhancement buy pills to make penis long erectile dysfunction pills without prescription natural penis enlargment without pills best male enhancement pills 2021 testosterone whats the best penis enhancement pills male libido boosters that work penis pills for size scientific penis enlargement super hard male sex enhancement philadelphia male enhancement pills

weight loss motivation mediterranean diet grocery list weight loss work out program keto boost pills reviews weight loss routine what is the most effective weight loss pill 12 week weight loss workout plan does cbd oil help with weight loss treadmill or elliptical for weight loss can you lose weight while breastfeeding southampton weight loss clinic double shot weight loss pills weight loss graph printable best over the counter diet pills uk college student weight loss with apple cider vinegar number 1 weight loss pill weight loss pittsburgh selling diet pills online weight loss smoothie recipes with whey protein best pre workout for weight loss can weed help you lose weight how much water to dr nk to lose weight avocado keto diet the best diet pills that really work prescription weight loss pills review stretching for weight loss diet pills near me post workout shake for weight loss can you eat sweet potatoes on a keto diet egcg pills weight loss can you eat buttered popcorn on the keto diet adr nal fatigue keto diet strongest fat burning pills pill weight loss chinese weight loss pills bee pollen vegan and weight loss gnc weight loss pills best whiskey on keto diet best weight loss pills to take apple cider for weight loss reviews chinese green tea pills weight loss clen pills weight loss where can i buy phentermine weight loss pills 600 calories a day weight loss results diet pills available in mexico best keto diet plan diet pills new amazing diet pills keto pills and blood thinners best all natural weight loss pill will water pills help u lose weight meal replacement shakes for weight loss

abcd cbd oil cbd oil sun shelf life of hemp seed oil south carolina state regulation on cbd oil pcos and cbd oil free sample cbd oil morphine and cbd oil what wattage is recommended for cbd oil does cbd oil work for trigeminal neuralgia how does cbd oil help pet seizures cbd oil dublin ireland gronks cbd oil best cbd oil tobuy in usa how to make cbd oil from alcohol buy cbd oil in california cbd oil ra cbd oil america schedule 1 pure cannabis oil for sale cbd oil in battle creek can you use oral cbd oil topically select cbd oil portland cbd oil pepperment drops will cbd oil cause a dirty drug test leweke cannabidiol testimonials on using cbd oil what cbd oil is best for arthritis pain cbd oil chenna cbd oil dose for migraine cbd oil eastern tennessee canine help llc cbd oil can cbd oil make me vomit cbd oil for joint pain mayo clinic is it legal for amazon to sell full spectrum cbd oil how often should you use cbd oil how does a retailer qualify to sell cbd oil cbd oil use review highest rated cbd oil amazon good lucl boadt cbd oil cbd oil and food interactions dr for cbd oil in los angeles epilepsy cbd oil near me can cbd oil have opposite effect cbd oil lies cbd oil at nutrition smart cbd oil makes memory worse cannabidiol fda lab results from cbd oil organic cbd oil without thc pg or vg purx cbd oil leg aches after cbd oil how much cbd oil for brachial neuritis cbd oil columbus ohio campus