WO2002027554A1

WO2002027554A1 - Electronic labbook

Info

Publication number: WO2002027554A1
Application number: PCT/US2001/029847
Authority: WO
Inventors: Shawn J. Green
Original assignee: Green Shawn J
Priority date: 2000-09-25
Filing date: 2001-09-25
Publication date: 2002-04-04

Abstract

The present invention is an electronic labbook (Figure 1) that is a vehicle for the recording of experimental research data and also acts as a portal to the internet wherein the present invention will query relevant databases based on the entry into the electronic labbook and will then store the retrieved information for the research to review at his or her convenience.

Description

ELECTRONIC LABBOOK

TECHNICAL FIELD

The present invention is a novel system and method for recording information on an electronic labbook and having the electronic labbook search the internet for information and vendors related to the information entered into the electronic labbook. In one embodiment, the present invention is a software application service provider and internet portal and browser in the fields of bioinformatics and biomedical informatics.

BACKGROUND OF THE INVENTION Prior art methods of recording information from experiments or other types of research usually involve simply entering the data into a book or onto a computer. The researcher than reviews the information, performs calculations and then, at a later time, will go to other sources to look up articles, patents and reviews that are related to the project that is being studied. The research will order necessary reagents and supplies as they are needed from a supply house. All of this activity takes a considerable amount of time.

What is needed is a system within which the researcher can enter data from experiments and the system then automatically selects key words from the entered data and queries the appropriate databases for relevant information.

SUMMARY OF THE INVENTION The present invention is an electronic labbook that smartly integrates data and relevant text-based information from both internal and external sources-including biomedical databases, scientific journals, and regulatory agencies-that biopharmaccutical companies need in their drug discovery and development decision-making. By combining an electronic lab book for capturing experimental results, with an underlying data warehouse architecture and internet portal, the present invention reduces the time required for research and contacting vendors for experimental supplies.

A unique attribute to the present invention is its ability to smartly query existing biomedical databases as new discoveries are unraveled in the lab. The researcher is confronted with endless data points, which need to be collected, stored, analyzed, cross-referenced, and analyzed again. The process is inefficient and costly, especially, if potentially new discoveries are delayed simply because of the failure to have access to timely and targeted-information. The present invention provides an internet portal coupled with its proprietary electronic note book and data mining software that accelerates and radically increases the likelihood of identifying relevant information to the researcher's project.

The present invention uses a combination of public domain and proprietary data structures that will allow for the cost-effective entry of data into the electronic labbook, while maximizing the use of widely supported and standardized technologies whenever possible.

The present invention wilt radically increase the likelihood of identifying potential drugs and therapies that are often missed or delayed in the discover process. In essence, experimental data and findings are constantly compared against the vast majority of other discoveries that are hidden away in the biomedical databases and medical libraries. In one embodiment of the present invention, the present invention has particular strength in the fields of cell biology, medicinal chemistry, molecular pathology, and intra-laboratory and interlaboratory or collaborative communication. In this embodiment, the present invention comprises an electronic lab book that runs under any browser and is designed to export to a variety of underlying databases that will support knowledge acquisition and import results-orientated information for a vast number of existing databases in the medical and biomedical community via the internet. These include a pathology database that supports molecular diagnostics, as well as, traditional laboratory testing. The present invention provides the basis for all subsequent steps in the drug research and development process, including, decision making for experimental design and testing, capturing new entities or potential drug candidates, identifying alternative uses of existing compounds, accelerating interpretation of new observations, providing supportive documentation for patent applications and regulatory filings to the FDA and other government agencies.

BRIEF DESCRIPTION OF THE FIGURES

Figure 1 is a schematic diagram of the prior art paradigm for drug discovery.

Figure 2 is a schematic diagram of the present invention.

DETAILED DESCRIPTION OF THE INVENTION

The present invention is a software application service provider and internet portal and browser in the fields of bioinformatics and biomedical informatics. The present invention can be used in the fields of cell biology, medicinal chemistry, drug discovery, clinical diagnostics, and project management.

In one embodiment, the present invention uses an

Extensible Markup Language (XML) compliant software system, with an underlying data warehouse architecture and internet portal, The present invention supplies the data mining and discovery tools of necessary to solve the researcher's need for better information and access to relevant data.

The present invention uses a combination of public domain and proprietary data structures that will allow for the cost-effective entry of data into its products while maximizing the use of widely supported and standardized technologies whenever possible. The result is a set of products that are scaleable, highly flexible in terms of the types of information that can be transferred and queried, and that financially leverage the user's expertise in biology and information systems in a manner that makes maximal use of available technologies and existing sources of biomedical information.

The present invention is an Extensible Markup Language-based (XML) electronic lab book implementation that runs under any XML enabled browser and is designed to export to a variety of underlying databases that will support knowledge acquisition and import results-orientated information for a vast number of existing databases in the medical and biomedical community via the internet. These include a pathology database that supports molecular diagnostics, as well as, traditional laboratory testing, and a unique response database that supports hypothesis driven queries relating to a drug's mechanism of action.

The present invention can optionally include an e- commerce set of inventory tools, a set of Internet search tools, and decision support systems. The present invention can be implemented across data generation platforms and is not limited to any vendor's products. A unique attribute to the present invention is the ability to smartly search existing relevant databases in the public domain as new discoveries are unraveled in the lab.

The present invention radically increases the likelihood of identifying potential drugs and therapies that are often missed or delayed in the discovery process. In essence, experimental data and findings are constantly compared against the vast majority of other discoveries in the biomedical databases and medical libraries.

Estimates of the current bioinformatics market is $300 million and is conservatively estimated to grow to $1 to $2 billion by 2002. This rapid growth in this field is driven by heavy research and development investment by pharmaceutical and biotechnology companies in areas including genomics, proteomics, and bioinformatics. Paralleling the growth of information systems has been an explosion in the raw quantity of data, the effective use of which will require new paradigms in biological research organization.

In addition to the large industrial market consisting of the major pharmaceuticals plus the biotechnology arena there is a substantial desktop market that covers the entire spectrum from the largest pharmaceutical client to academic and educational end users. The present invention will simultaneously address both ends of this market spectrum by offering a basic electronic lab note book that will enable desk top databases of experimental designs and results to the low end of the market, while offering in addition, consulting services and database integration services to the high end customer.

Most bioinformatics systems have focused on sequence data as the primary type of information its customers wish to interpret. However, biological research is undergoing a metamorphosis away from gene isolation toward a more quantitative field in which the interrelationships between pathways is stressed. The sequenced-based information systems currently in use are not optimized to support these needs and a new systems approach is required. The present invention with its corresponding database services can vastly increase the pharmaceutical research investment because they are searchable in a manner that allows scientist to construct queries that are relevant to biological hypothesis, retrieve quantitative data, and are consistent across repositories, thus enabling web based agent technology to be used for knowledge-discovery purposes. By building in a molecular pathology database, the present invention also expands into the medical informatics and clinical trials-based markets. Thus, the present invention will not compete directly against the bulk of the market, but will forward integrate towards the clinical trial markets as it builds its foundation in the early stages of discovery, research, and development.

Figure 1 is a schematic of the conventional manner of performing research. The researcher will typically perform experiments and then, after analyzing the results of the research will then perform the indicated independent steps. For example, after review the data collected from an experiment, the research will typically perform manual searches of relevant journals to obtain articles that are related to the experiments performed. The researcher may consult manually with genomic and cellular databases; he or she may manually and independently order supplies from a variety of vendors; and, he or she may consult with the patent databases to determine the novelty of his or her invention. All of these activities are very time consuming and are not comprehensive.

Figure 2 is a schematic of one embodiment of the present invention. The research enters the data into the electronic labbook (labbook.com) and the software that is part of the present invention will recognize key words in the labbook entry and will query the relevant databases, e.g., scientific journals, patent databases and genomic and cellular databases. If the researcher requires certain reagents or other supplies, he or she simply enters the name of the reagent or supply into the electronic labbook, which can be a tab in the electronic labbook, and the program sends an order over the internet to appropriate vendors.

It is to be understood that the present invention is not limited to medical, biomedical or chemical applications but can be adapted to a wide variety of disciplines, including but not limited to, electronics research, sales, accounting and the like.

Claims

CLAIMS:What is claimed is:

1. An electronic resource and information search, retrieval and integration method, comprising: entering data into an electronic document; optionally employing a protocol for integrating, manipulating and/or calculating the data; and employing a protocol for: selecting key words from the data and querying data bases for information related to the selected key words; capturing, importing and integrating the information related to the selected key words into the electronic document; and manipulating and/or calculating the data with the information related to the selected key words.

2. The method of claim 1 wherein the data is chosen from the group comprising biological, bioinformatic, biopharmacological and biomedical data.

3. The method of claim 1 wherein the data is chosen from the group comprising genomic, text-based information and laboratory results.

4. The method of claim 1 wherein the information related to the selected key words is chosen from the group comprising articles, patents, reviews, vendors, supply houses, libraries, biomedical databases, scientific journals, regulatory agencies, public domain databases, proprietary databases, genomic databases, and cellular databases.