Protein Data Integration through Ontologies

In this paper, we consider the challenges of information integration in proteomics from the prospective of researchers using information technology as an integral part of their discovery process. Specifically, data integration, metadata specification, data provenance and data quality are discussed here. Here we review existing protein data integration methods and propose the use of common vocabulary for protein data integration using ontologies

Protein ontology development using OWL

To efficiently represent the protein annotation framework and to integrate all the existing data representations into a standardized protein data specification for the bioinformatics community, the protein ontology need to be represented in a format that not enforce semantic constraints on protein data, but can also facilitate reasoning tasks on protein data using semantic query algebra. This motivates the representation of Protein Ontology (PO) Model in Web Ontology Language (OWL). In this paper we briefly discuss the usage of OWL in achieving the objectives of Protein Ontology Project. We provide a brief overview of Protein Ontology (PO) to start with. In the later sections discuss why OWL was an ideal choice for PO Development

OWL, proteins and data integration

In this paper, we propose an approach to integrate protein information from various data sources by defining a Protein Ontology. Protein Ontology provides the technical and scientific infrastructure and knowledge to allow description and analysis of relationships between various proteins. Protein Ontology uses relevant protein data sources of information like PDB, SCOP, and OMIM. Protein Ontology describes: Protein Sequence and Structure Information, Protein Folding Process, Cellular Functions of Proteins, Molecular Bindings internal and external to Proteins, and Constraints affecting the Final Protein Conformation. Details about Protein Ontology are available online at http://www.proteinontology.info/

Ontology-based Knowledge Representation for Protein Data

The advances in information and communication technologies coupled with increased knowledge about genes and proteins have opened new perspectives for study of protein complexes. There is a growing need to integrate the knowledge about various protein complexes for effective disease prevention mechanisms, individualized medicines and treatments and other accepts of healthcare. In this paper we propose a protein ontology that handles the following computational challenges in the area proteomics and systems biology in general: (1) it provides more accurate interpretations and associations as conclusions are based on data and semantics. (2) It makes it possible to study relationships among proteins, protein folding, behaviour of protein under various environments, and most importantly cellular function of protein. This protein ontology is a unified terminology description integrating various protein database schemas and provides a easier way to predict and understand proteins

Protein ontology: Vocabulary for protein data

These Huge amounts of Protein Structure Data make it difficult to create explanatory and predictive models that are consistent with huge volume of data. Difficulty increase when large variety of heterogeneous approaches gathers data from multiple perspectives. In order to facilitate computational processing data, it is especially critical to develop standardized structured data representation model formats for proteomics data. In this paper we describe a Protein Ontology Model for integrating protein databases and deduce a structured vocabulary for understanding process of protein synthesis completely. Proposed Protein Ontology Model provides biologists and scientists with a description of sequence, structure and functions of protein and also provides interpretation of various factors on final protein structure conformation. The Structured Vocabulary for Protein Data, describing Protein Ontology is composed of various Type Definitions for Protein Entry Details, Sequence and Structural Information of Proteins, Structural Domain Family of Protein, Cellular Function of Protein, Chemical Bonds present in the Protein, and External Constraints deciding final protein conformation. The Proposed Ontology Model will provide easier ways to predict and understand proteins

Protein Ontology Project: 2006 updates

Protein Ontology (PO) is a means of formalizing protein data and knowledge; protein ontology includes concepts or terms relevant to the domain, definitions of concepts, and defined relationships between the concepts. PO integrates protein data formats and provides a structured and unified vocabulary to represent protein synthesis concepts. PO provides integration of heterogeneous protein and biological data sources. This paper discusses the updates that happened to the Protein Ontology Project since it was last presented at the Data Mining 2005 Conference

An Aboriginal English Ontology Framework for Patient-Practitioner Interview Encounters

Current diagnosis, treatment and healthcare delivery processes in Australia are dominated by long established westernized clinically driven methods of patient-practitioner interaction. Consequently this dominant healthcare provider influence contributes to risk of miscommunication, misinformation in patient records and reciprocal misunderstandings that go unrecognised as such. For Indigenous communities, inadequate health literacy (HL) and a pervasive semantic disconnect are major barriers. Overcoming these barriers in the primary care setting presents opportunities to deliver appropriate timely and more effective care. We propose an e-health framework that enhances the Patient-Practitioner Interview Encounter (PPIE) through the use of a patient-centric linguistic interface using semantic mappings between Aboriginal English (AE) and Standard Australian English (SAE). This will ameliorate communications and interactions, so meeting the needs of all stakeholders (Patients, Physicians, Nurses, Allied Health Professionals and their Non-Critical Carers) engaged in Indigenous patient-centric primary care. It provides healthcare practitioners and their Indigenous T2DM patients with a new platform for two-way educative sharing and knowledge exchange that will increase mutually productive treatment, care and management expectations

A PACS alternative for transmitting DICOM images in a high latency environment

Picture Archiving and Communication System(PACS) is responsible for storing Digital Imaging and Communication in Medicine (DICOM) images fromradiology modalities into its database, images takes a lot of time to transfer to remote location through WAN due to large file size and slow transfer protocol. A PACS alternative system has been developed which performs basic functions of a generic PACS. Images directly from modalities are large in size by default transfer syntax of these images is Endian Explicit syntax. Changing this transfer syntax to lossless JPEG 2000 decreases the file size and because of lossless compression quality of image is still same as original image. These compressed images are then copied into Network Attached Storage working as PACS alternative. A series of test conducted in lab with multiple transfer protocol on Network Attached Storage (NAS) to find out which transfer protocol is faster under moderate speed and high latency network

A Framework for Patient Practitioner Information Exchange

The global Type 2 Diabetes Mellitus (T2DM) epidemic imposes a heavy burden on communities that are ethnically vulnerable to the disease and further disadvantaged by socio-economic circumstance and cultural communications barriers. Aboriginal communities in rural and remote Western Australia are representative of these high-riskgroups. Indigenous patients needing continuous management of T2DM are also experiencing disproportionate risk of co-morbidities and hospitalizations compared with nonindigenous patients. Type 2 Diabetes Mellitus (T2DM) is often described as ’the lifestyle disease’. Within clinical care and patient quality of life management domains, T2DM presents both the healthcare practitioner and the patient with a mosaic of complexities.Information processing demands for self-management of diabetes are extensive, requiring constant self monitoring and assessment of the illness state in order to apply per instance and per condition the most appropriate form of control. In this work we introduce a primary care communications concept tool centered upon optimization of the Patient-Practitioner Interview Encounter (PPIE). The target beneficiary is the Aboriginal T2DM patient living in Western Australia. Avital part of our design effort is therefore dedicated to understanding and responding to the cultural domain barriers, challenges and opportunities of this specific health care environment

Coupling of indigenous-patient-friendly cultural communications with clinical care guidelines for type 2 diabetes mellitus

Distance, terrain, climate and inadequate medical resources seriously constrain health care accessibility for rural and remote Indigenous communities of Western Australia (WA). Management of the Type 2 Diabetes Mellitus (T2DM), a chronic condition affecting Indigenous people much more than non-Indigenous, requires a complex assortment of time-sensitive communications activity and interventions to avert serious complications. Communications barriers arising from pervasive cultural misunderstanding in primary care go far beyond language differences and routine translation techniques. Practitioners and patients lacking the capability and capacity to facilitate dialogue for shared meaning in the examination and testing discourse need a culturally sensitive purpose-driven informatics system of support for the Patient-Practitioner Interview Encounter (PPIE). The dominant unidirectional clinician-biased forms of communication employed by healthcare professionals are a major barrier. Our developing communications support model utilizes the mapping of ontologies. The Community Healthcare ontology is dedicated to mapping a clinical taxonomy for T2DM national guidelines to Aboriginal English (AE). The eventual user interface will represent Aboriginal patient-culture-driven access to and use of interactive audio visual media in the primary healthcare setting.This research objective establishes value of and respect for the Aboriginal patient’s dialectal and pragmatic preferences, thereby enabling us to couple these preferences with Australia’s Standard English clinical communications practice in the treatment and care of IndigenousT2DM patients. A critical capability of the eventual application, especially when phrase ontology guidance enters the interface will be the interception of ambiguities and mitigation of misinterpretation risk. The emphasis is concentrated on bi-directional communications assistance that will not only enhance the Aboriginal patient opportunity to contribute to the PPIE, but will reinforce the value of and reciprocal respect for, sound clinical practice