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Method for automating the probe construction and consolidated automatic entry from instruments into LIMS database, for a gene expression experiment, using a set of Web Services workflow

IP.com Disclosure Number: IPCOM000016188D
Original Publication Date: 2002-Nov-23
Included in the Prior Art Database: 2003-Jun-21
Document File: 3 page(s) / 102K

Publishing Venue

IBM

Abstract

This publication describes a method for automating the probe construction and consolidated automatic entry from instruments into LIMS database, for a gene expression experiment, using a set of Web Services workflow. The Micro array construction and management involves tracking of the clones, probes, and various lab procedures. Currently in most cases the clone information is either in excel spreadsheet or Microsoft Access database. In addition the scientist also needs to track various instruments used during this process of preparing probes. For example, he/she may use spectrophotometer to measure the amount of fluorescence. The instrument needs to be calibrated and other details of the data collection should be tracked. Various robots are used to spot the probes on the slides, the liquid dispensed should be tracked and if there is an error it will not be noticed till we obtain the final result, which would be days to couple of weeks depending on the experiment. Data acquisition requires tracking of the information of the target used for the experiment and recording the experimental details of the fluorescent labeling procedure. The fluorescence from the target is what is detected. The chips are scanned in scanners and the images are stored on zip disks or CD-ROM for further analysis. One needs to manage these files disks. Sometimes this data is moved between different institutions. Normalization may help correcting scanned intensities for inherent biases in the system. The novel approach used in this disclosure defines Web Services for each set of tasks for the Micro array data management problem, and then suggests definition of a workflow in Web Service Flow Language to initiate the defined Web Services in the correct order. The set of the web services chained together in a web service flow, could automate the data management of the copious data from the micro array experiment. Web Services Used 1 Reagent Data Tracking

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  Method for automating the probe construction and consolidated automatic entry from instruments into LIMS database, for a gene expression experiment, using a set of Web Services workflow

    This publication describes a method for automating the probe construction and consolidated automatic entry from instruments into LIMS database, for a gene expression experiment, using a set of Web Services workflow.

The Micro array construction and management involves tracking of the clones, probes, and various lab procedures. Currently in most cases the clone information is either in excel spreadsheet or Microsoft Access database. In addition the scientist also needs to track various instruments used during this process of preparing probes. For example, he/she may use spectrophotometer to measure the amount of fluorescence. The instrument needs to be calibrated and other details of the data collection should be tracked. Various robots are used to spot the probes on the slides, the liquid dispensed should be tracked and if there is an error it will not be noticed till we obtain the final result, which would be days to couple of weeks depending on the experiment. Data acquisition requires tracking of the information of the target used for the experiment and recording the experimental details of the fluorescent labeling procedure. The fluorescence from the target is what is detected. The chips are scanned in scanners and the images are stored on zip disks or CD-ROM for further analysis. One needs to manage these files & disks. Sometimes this data is moved between different institutions. Normalization may help correcting scanned intensities for inherent biases in the system.

The novel approach used in this disclosure defines Web Services for each set of tasks for the Micro array data management problem, and then suggests definition of a workflow in Web Service Flow Language to initiate the defined Web Services in the correct order. The set of the web services chained together in a web service flow, could automate the data management of the copious data from the micro array experiment.

Web Services Used 1 Reagent Data Tracking

Description: The technician in the laboratory has to track the process of the micro array construction which involves person, reagents, instruments, supplies used. Normally a laboratory information management system (LIMS) is used. Experimental details of the chips also needs to be tracked.

Input: Annotation data for each probe

Output: An updated LIMS database with one entry for each probe, and experimental details of the target used in the experiment.

2 Data Generation and Normalization

Description: After the labeling and hybridization steps the microarray chips are scanned. There are different types of scanners i.e. Laser scanning confocal microscope, or a charged coupled device. This web service takes the images scanned from each probe on the gene chip in terms of 'raw' spectral magnitude, and creates a database with image, sp...