Om Chan - Academia.edu (original) (raw)

Papers by Om Chan

Baru saja bangun dari tidur q jam 00.34 tadi di hp q, penuh keringat dengan bayang masih dalam mi... more Baru saja bangun dari tidur q jam 00.34 tadi di hp q, penuh keringat dengan bayang masih dalam mimpi yang agak aneh tapi tak menakutkan, agak bingung bangun tidur tengah tengah malam begini dengan tak sengaja tertidur selesei pengajian tadi.

Bioinformatics/computer Applications in The Biosciences, 2004

Motivation: To promote a systems biology approach to understanding the biological effects of envi... more Motivation: To promote a systems biology approach to understanding the biological effects of environmental stressors, the Chemical Effects in Biological Systems (CEBS) knowledge base is being developed to house data from multiple complex data streams in a systems friendly manner that will accommodate extensive querying from users. Unified data representation via a single object model will greatly aid in integrating data storage and management, and facilitate reuse of software to analyze and display data resulting from diverse differential expression or differential profile technologies. Data streams include, but are not limited to, gene expression analysis (transcriptomics), protein expression and protein-protein interaction analysis (proteomics) and changes in low molecular weight metabolite levels (metabolomics). Results: To enable the integration of microarray gene expression, proteomics and metabolomics data in the CEBS system, we designed an object model, Systems Biology Object Model (SysBio-OM). The model is comprehensive and leverages other open source efforts, namely the Micro-Array Gene Expression Object Model (MAGE-OM) and the Proteomics Experiment Data Repository (PEDRo) object model. SysBio-OM is designed by extending MAGE-OM to represent protein expression data elements (including those from PEDRo), protein-protein interaction and metabolomics data. SysBio-OM promotes the standardization of data representation and data quality by facilitating the capture of the minimum annotation required for an experiment. Such standardization refines the accuracy of data mining and interpretation. The * To whom correspondence should be addressed. † The authors wish it to be known that, in their opinion, these two authors should be regarded as joint First Authors. open source SysBio-OM model, which can be implemented on varied computing platforms is presented here. Availability: A universal modeling language depiction of the entire SysBio-OM is available at http://cebs.niehs.nih.gov/ SysBioOM/. The Rational Rose object model package is distributed under an open source license that permits unrestricted academic and commercial use and is available at http://cebs.niehs.nih.gov/cebsdownloads. The database and interface are being built to implement the model and will be available for public use at http://cebs.niehs.nih.gov.

Biodrugs, 1999

More than a century ago, Jonathan Hutchingson, a surgeon-dermatologist, identified the first case... more More than a century ago, Jonathan Hutchingson, a surgeon-dermatologist, identified the first case of sarcoidosis at King's College, London. The disease is now known as a commonplace multi-system disorder characterised by the formation of noncaseating granulomata. The diagnosis of sarcoidosis is established by recognising clinicoradiological findings and providing histological evidence of noncaseating granuloma. Serum angiotensin converting enzyme levels are high in about two-thirds of the patients and hypercalcaemia is a feature in 1 of every 10 patients with sarcoidosis. Immunological abnormalities include depression of cutaneous delayed-type hypersensitivity, hyperactive B cells and the presence of circulating immune complexes. The course and prognosis of the disease usually correlate with the mode of onset. An acute onset with erythema nodosum indicates a good prognosis and spontaneous resolution, whereas an insidious onset may be followed by relentless, progressive fibrosis. Mortality and morbidity are caused by pulmonary fibrosis, cardiac arrhythmias, renal failure, neurological involvement and blindness. Corticosteroids and choloroquine relieve symptoms and suppress inflammation and granuloma formation.

Baru saja bangun dari tidur q jam 00.34 tadi di hp q, penuh keringat dengan bayang masih dalam mi... more Baru saja bangun dari tidur q jam 00.34 tadi di hp q, penuh keringat dengan bayang masih dalam mimpi yang agak aneh tapi tak menakutkan, agak bingung bangun tidur tengah tengah malam begini dengan tak sengaja tertidur selesei pengajian tadi.

Baru saja bangun dari tidur q jam 00.34 tadi di hp q, penuh keringat dengan bayang masih dalam mi... more Baru saja bangun dari tidur q jam 00.34 tadi di hp q, penuh keringat dengan bayang masih dalam mimpi yang agak aneh tapi tak menakutkan, agak bingung bangun tidur tengah tengah malam begini dengan tak sengaja tertidur selesei pengajian tadi.

Bioinformatics/computer Applications in The Biosciences, 2004

Motivation: To promote a systems biology approach to understanding the biological effects of envi... more Motivation: To promote a systems biology approach to understanding the biological effects of environmental stressors, the Chemical Effects in Biological Systems (CEBS) knowledge base is being developed to house data from multiple complex data streams in a systems friendly manner that will accommodate extensive querying from users. Unified data representation via a single object model will greatly aid in integrating data storage and management, and facilitate reuse of software to analyze and display data resulting from diverse differential expression or differential profile technologies. Data streams include, but are not limited to, gene expression analysis (transcriptomics), protein expression and protein-protein interaction analysis (proteomics) and changes in low molecular weight metabolite levels (metabolomics). Results: To enable the integration of microarray gene expression, proteomics and metabolomics data in the CEBS system, we designed an object model, Systems Biology Object Model (SysBio-OM). The model is comprehensive and leverages other open source efforts, namely the Micro-Array Gene Expression Object Model (MAGE-OM) and the Proteomics Experiment Data Repository (PEDRo) object model. SysBio-OM is designed by extending MAGE-OM to represent protein expression data elements (including those from PEDRo), protein-protein interaction and metabolomics data. SysBio-OM promotes the standardization of data representation and data quality by facilitating the capture of the minimum annotation required for an experiment. Such standardization refines the accuracy of data mining and interpretation. The * To whom correspondence should be addressed. † The authors wish it to be known that, in their opinion, these two authors should be regarded as joint First Authors. open source SysBio-OM model, which can be implemented on varied computing platforms is presented here. Availability: A universal modeling language depiction of the entire SysBio-OM is available at http://cebs.niehs.nih.gov/ SysBioOM/. The Rational Rose object model package is distributed under an open source license that permits unrestricted academic and commercial use and is available at http://cebs.niehs.nih.gov/cebsdownloads. The database and interface are being built to implement the model and will be available for public use at http://cebs.niehs.nih.gov.

Biodrugs, 1999

More than a century ago, Jonathan Hutchingson, a surgeon-dermatologist, identified the first case... more More than a century ago, Jonathan Hutchingson, a surgeon-dermatologist, identified the first case of sarcoidosis at King's College, London. The disease is now known as a commonplace multi-system disorder characterised by the formation of noncaseating granulomata. The diagnosis of sarcoidosis is established by recognising clinicoradiological findings and providing histological evidence of noncaseating granuloma. Serum angiotensin converting enzyme levels are high in about two-thirds of the patients and hypercalcaemia is a feature in 1 of every 10 patients with sarcoidosis. Immunological abnormalities include depression of cutaneous delayed-type hypersensitivity, hyperactive B cells and the presence of circulating immune complexes. The course and prognosis of the disease usually correlate with the mode of onset. An acute onset with erythema nodosum indicates a good prognosis and spontaneous resolution, whereas an insidious onset may be followed by relentless, progressive fibrosis. Mortality and morbidity are caused by pulmonary fibrosis, cardiac arrhythmias, renal failure, neurological involvement and blindness. Corticosteroids and choloroquine relieve symptoms and suppress inflammation and granuloma formation.

Baru saja bangun dari tidur q jam 00.34 tadi di hp q, penuh keringat dengan bayang masih dalam mi... more Baru saja bangun dari tidur q jam 00.34 tadi di hp q, penuh keringat dengan bayang masih dalam mimpi yang agak aneh tapi tak menakutkan, agak bingung bangun tidur tengah tengah malam begini dengan tak sengaja tertidur selesei pengajian tadi.