NL2030706A - Establishment method of comparative medicine big data platform - Google Patents

Abstract

Purpose: a first comparative medicine big data platform service system of at home and abroad is established to provide services for researchers to obtain effective scientific data of laboratory animals and animal models, provide data support for decision makers, and solve the problems of data acquisition and analysis in research. Methods: metadata and data collection related forms are developed, laboratory animal related data and comparative medicine related data resources are integrated, and the large—scale laboratory animals, animal models, phenotypic data and animal experimental data are integrated to build a comparative medicine big data platform based on PHP. Results: based on relevant research results of comparative medicine at home and abroad, the comparative medicine big data. platforml https://com—med.org.cn/) systematically combs the laboratory animals, animal models and animal experimental data, forms results of multi—dimensional cross temporal and spatial data comparison and analysis.

Description

P1052 /NLpd

ESTABLISHMENT METHOD OF COMPARATIVE MEDICINE BIG DATA PLATFORM

TECHNICAL FIELD The present disclosure belongs to a field of big data plat- form establishment.

BACKGROUND ART The life science and modern medicine in developed countries such as Europe and the United States started earlier, and they have a deep understanding of the strategic position of laboratory animals and human disease animal models in relevant scientific re- search and industrial development, and their software and hardware platform construction and management system are relatively com- plete. A large number of laboratory animal databases and infor- mation resource platforms have been established to realize data resource sharing. For example, " mouse genome information (MGI), "mouse phenotype database (MPD)", "gene expression database (GXD)", "mouse tumor biology database (MTB)}", etc. of Jackson La- boratory in the United States. Rat genome database (RGD) and ani- mal model and human disease association database (LAMHDI) of NIH in the United States. The UK has a "rodent genome database", "mouse cell genetic map", "deformed human mouse homology data- base", and the European mouse mutation resource bank (INFRAFRON- TIER) to share laboratory animal strain resources and related re- search data.

Because China has not improved the comparative medicine big data platform before, there have been many problems in the field of human disease animal model and comparative medicine in the past three decades, such as project-oriented, loss of relevant re- sources, data and information, and a large number of duplication and waste due to the lack of centralized resources and imperfect sharing system. Researchers and medical workers can only under- stand through articles when purchasing susceptible animal re- sources and disease animal model resources, which creates a "bar- rier" for the acquisition and application of disease animal mod-

els. Research on laboratory animal resources and animal models in China lacks a large-scale resource database or big data platform. The establishment of a comparative medicine big data platform , the preservation and effective sharing of these resources and data are of great significance to promote the research and prevention of human diseases.

Relying on rich laboratory animal resources and comparative medicine research data resources, the comparative medicine big da- ta platform faces the major strategic needs of the sustainable de- velopment of China's life science, biomedicine and laboratory ani- mal industry, establishes a big data storage, integration, mining, analysis and research system for laboratory animals and compara- tive medicine, and develops a big data collection, sharing and management platform for laboratory animals, builds a well-known laboratory animal science data center to support the development of China's life science, biomedicine and laboratory animal indus- tries.

There is no big data platform in the world, which can include laboratory animal resources, animal models, animal experiments, animal phenotypes and comparative medicine big data. The compara- tive medicine big data platform realizes the integration and shar- ing of scientific data resources related to comparative medicine. By mobilizing the scattered animal model resources of various in- stitutions, gather parts into a whole, and the results and the da- ta resources related to comparative medicine at home and abroad are gathered. The supporting capacity of the comparative medicine big data platform are enlarged to form a supporting scientific da- ta platform for animal models of human diseases, which has the ability to select or develop animal models according to the re- search needs of medical problems.

SUMMARY The establishment method of comparative medicine big data platform of the present disclosure includes the following steps:

1.1 Collecting data source; Original data of the platform comes from data owned by an In- stitute of Medical Laboratory Animals of Chinese Academy of Medi-

cal Sciences, Laboratory Animal Research Institute, as well as published journal literature, book monographs, public databases and research reports; after a demonstration of an expert group, metadata and data collection related tables are formulated, and a data structure and a data standard are determined; the data is re- viewed and confirmed by experts in a field of comparative medicine and included in a database to ensure data quality.

1.2 Establishing a database The comparative medicine big data platform uses phpStudy to configure the environment and distributed information processing is performed based on B/S (Browser/Server) architecture; each node is distributed on the network and functional tasks is completed through browser side, server side and middleware link and interac- tion; RBAC (role-based access control) is designed for role-based permission management, access control of system functions is real- ized through roles, and the roles are associated with permissions; MySQL database is installed, SQL script is written and database test is performed; the browser interacts with the database through web server, and a platform is established for joint query of mul- tiple sub databases and display of laboratory animal information. By integrating comparative medicine related data resources, formulate metadata, data collection specifications and related forms. Subject databases of the platform includes: laboratory ani- mal resource database (laboratory animal species database, labora- tory animal strain database, laboratory animal biological charac- teristics database, genetic engineering animal database), disease animal model database (animal model database, infectious disease animal model database, degenerative disease animal model database, coronavirus infection animal model database), series of compara- tive medicine databases (comparative disease database, comparative physiology database, comparative biochemistry database, compara- tive pathology database, comparative imaging database, comparative behavior database, comparative gene and phenotype database, com- parative microbiology database, comparative anatomy database, com- parative medicine literature database), series of comparative ge- nomics databases (comparative genomics database of coronavirus in- fected animal models, comparative genomics database of influenza animal models, comparative genomics database of heart disease ani- mal models, and big data management system of comparative medical omics), laboratory animal ontology database (laboratory animal al- ternative database, laboratory animal noun ontology database, com- parative infectious disease knowledge base, infectious disease an- imal model knowledge base), series of animal experiment databases (animal experiment database, laboratory animal technology data- base, animal model drug screen database), laboratory animal prod- uct database (laboratory animal product database), laboratory ani- mal related database (laboratory animal facility database).

1.3 visiting method The website of the comparative medical big data platform: https://com-med.org.cn/. It is publicly available and free to use.

BRIEF DESCRIPTION OF THE DRAWINGS Fig. 1 is an architecture of a comparative medicine big data platform. Fig. 2 is a home page of the comparative medicine big data platform. Fig. 3 is a data sub-database of the comparative medicine big data platform. Fig. 4 is a comparative analysis function of the comparative medicine big data platform. Fig. 5 is a bioinformatics tool of the comparative medicine big data platform. Fig. 6 is external resources of the comparative medicine big data platform.

DETAILED DESCRIPTION OF THE EMBODIMENTS

2.1 An architecture of a comparative medicine big data plat- form The big data platform system for comparative medicine is di- vided into four layers: a data source layer, a data extraction layer, a data storage layer, an application layer, and supporting functions such as user management and system monitoring (Fig. 1). (1) The data source layer mainly includes various source data generated by comparative medical research, including experimental data, and processes of data collection, input, integration, pro- cessing, storage and release for a purpose of data analysis and sharing. (2) The data extraction layer mainly includes several pro- 5 cesses such as data collection, transmission, verification, con- version, and loading from internal and external data sources to the comparative medicine big data platform .

(3) The data storage layer includes cache database and data warehouse. {4) The application layer consists of data analysis and data display. (5) The web portal (Fig. 2) facilitates users to enter, query and analyze data through a browser. (6) Users are classified according to their roles and the permissions are controlled. (7) System security monitoring includes: network monitoring, server monitoring, database monitoring and log monitoring. (8) Data backup mechanism is provided to ensure the stability and reliability of the whole system.

2.2 Subject databases The comparative medicine big data platform includes 30 sub databases (Fig. 3), including 19 platform subject databases (Table 1), which provide functions such as query, display, data entry, data review, etc. There are 11 external chain sub libraries, which are the sub libraries of the framework system of comparative medi- cine. The platform subject databases realize the correlation of data entries through the associated model, strain, species and mi- croorganism database. Users can click to view the associated data. Table 1 subject databases of comparative medicine big data platform laboratory animal species name, classification, feature de- species database scription, genome, proteome, references, pictures. laboratory animal laboratory animal strain name, species, strain database category, genotype, description, passage,

appearance characteristics, genetic charac- teristics, breeding process, related sub- lines, pictures, biological characteris- tics, life span and disease, application field, feeding and reproduction, seed con- servation unit and references. animal model data- animal model name, species, strain, human base disease, infectivity, microorganism, cate- gory, modeling factors, manufacturing meth- ods, evaluation criteria, biological char- acteristics, medical uses, clinical mani- festations, pathogenesis, clinical diagno- sis, preservation unit and references. laboratory animal the name, type classification, related pic- alternative data- tures, subject scope, method description, base performance evaluation, purchase price, ap- plication field, production unit, supplier, provider, and reference of the laboratory animal substitute product or method. laboratory animal general description, physiological traits, biological charac- anatomical traits, hematological traits, teristics database |blood biochemical traits, urinary biochemi- cal traits, reproductive traits, genetic traits, immunological traits, spontaneous tumors, spontaneous abnormalities, feed nu- trition, providers and references. genetic engineering genetic engineering animal name, gene in- animal database formation, disease name, strain type, pro- duction method, background strain, pheno- typic characteristics, primer sequence, ap- plication field, reproduction mode, preser- vation status, provider, provider and ref- erence. laboratory animal animal related facility name, facility cat- facility database egory, facility address, industry, license, license scope, facility introduction, fa-

cility management, business scope, labora- tory animals, resource supply, technical specifications, facility equipment, scien- tific and technological achievements, us- ers, providers and reference documents.

comparative disease human disease name, alias, category, ICD-10 database number, OMIM number, MeSH number, DO num- ber, infectious disease, microorganism, overview, epidemiology, etiology, pathogen- esis, clinical manifestation, clinical stage, complications, clinical diagnosis and literature.

comparative physi- information data such as laboratory animal ology database name, disease name, gender, age, weight, body temperature, total blood volume, whole blood specific gravity, systolic blood pressure, etc.

comparative bio- laboratory animal name, disease name, total chemistry database bilirubin, indirect bilirubin, direct bili- rubin, urea nitrogen, creatinine (serum), creatine, uric acid and other information data.

comparative pathol- | animal model name, disease name, pathologi- ogy database cal map, pathological characteristics and references.

comparative imag- animal model name, disease name, image eology database type, image, image feature description and references.

comparative gene gene name, gene number, other names, spe- and phenotype data- | cies, mapping, phenotypic analysis, go base analysis, pathway analysis, references.

comparative micro- |microbial name, genus name, historical biology database source, NCBI species number, separation me- dium, culture medium, main characteristics, preservation method, biological hazard, physical state, sharing mode and refer-

Ee comparative anatomy | laboratory animal name, general descrip- database tion, gross anatomy, organ weight, skeletal system, digestive system, respiratory sys- tem, lymphatic system, circulatory system, nervous system, reproductive system, endo- crine system, provider and references. comparative medical | literature name, PMID number, author, Chi- literature database | nese abstract, English abstract, key words, publication journal, publication year. animal experiment experimental name, English name, experi- database mental classification, industry, license, IACUC, experimental background, experi- mental purpose, experimental methods, la- boratory animals, animal welfare, opera- tors, experimental conditions, experimental results, statistical analysis, main conclu- sions, result discussion, providers and references. laboratory animal experimental technology name, technical technology database principle, technical method, operation ex- ample, technical application, achievement display, references and other information. laboratory animal product name, English name, product classi- product database fication, origin/brand, product specifica- tion, function introduction, manufacturing method, product standard, performance pa- rameters, application field, manufacturer, distributor, reference quotation, provider and references.

2.3 Comparative analysis The comparative analysis function can retrieve the data of 6 sub databases of comparative physiology, comparative biochemistry, comparative pathology, comparative image, comparative behavior and comparative anatomy through the model, and compare the same type of data in the form of multiple columns on one page. Each attrib- ute has one row, and the comparison results show red for the same data and black for different data (Fig. 4).

2.4 Bioinformatics tools of comparative medicine big data platform The "analysis tools" column of the comparative medicine big data platform integrates bioinformatics tools according to com- parison tools, interaction tools, prediction tools, enrichment tools and mapping tools, including classification directory, tool list and detail page (Fig. 5).

2.5 External resources of comparative medicine big data plat- form The "external resources” column of the big data platform for comparative medical include databases related to laboratory ani- mals according classification of genome database, gene expression database, transcriptomics database, proteomics database, protein interaction database, metabonomics database, laboratory animal re- source database, human disease database.

The contents of the database directory list include: database name, introduction, keywords, website, which can be linked to cor- responding databases. The left side is the database classification navigation bar, and the right side is the database browsing list. Click the list to open the corresponding details page. It can be retrieved by title, keywords, introduction, and can be continuous- ly entered into a new database through the website backend (Fig. 6).

Claims (3)

CONCLUSIONS A method for setting up a big data platform for comparative medicine, the method comprising the steps of: 31, collecting data source; 52, setting up a database; S3, visiting a big data platform website for comparative medicine: https://com-med.org.cn/. The method of claim 1, wherein the step S1 comprises: original data is from data owned by an Institute of Medical Experimental Animals of the Chinese Academy of Medical Sciences, Research Institute of Laboratory Animals, as well as published journal literature, book monographs, graphs, public databases and research reports; after a demonstration by an expert group, metadata and data collection related tables are prepared and a data structure and a data standard are determined; the data are reviewed and corroborated by experts in the field of comparative medicine and entered into a database. The method of claim 1, wherein step S2 comprises: the big data comparative medicine platform uses phpStudy to configure the environment and distributed information processing is performed based on B/S (Browser/Server) architecture; each node is distributed on the network and functional tasks are completed through browser side, server side and middleware link and interaction; RBAC (role-based access control) is designed for role-based permission management, access control of system functions is realized through roles, and the roles are associated with permissions; MySQL database is installed, SQL script is written and database test is performed; the browser communicates with the database via a web server, and a platform is set up for jointly querying multiple sub-databases and displaying information about laboratory animals.