Description of the OOCDB
Intellectual property involved of the data sources
Comprehensive Report
The data sources of OOCDB databases are all open access databases, and the downloading and mining of data are carried out in accordance with the instructions and copyright policies of each public database. For the non-local content in the database, OOCDB only provides the title, abstract and other related information, and does not contain the full text of the articles. The original resources and links are also prominently provided to facilitate researchers' access to the original website. Detailed instructions for copyright information are available in the HELP interface of OOCDB.
Data Sources
| Source# | Data Sources | External Links | Description |
|---|---|---|---|
| 1 | PubMed | https://pubmed.ncbi.nlm.nih.gov/ | PubMed® comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. |
| 2 | Fda(food and drug administration) | https://www.fda.gov/ | The FDA provides information gathered from press releases and other public notices about certain recalls of FDA-regulated products. Not all recalls have press releases or are posted on this website. |
| 3 | PubChem | https://pubchem.ncbi.nlm.nih.gov/ | PubChem is an open chemistry database at the National Institutes of Health (NIH). |
| 4 | TogoWS | http://togows.dbcls.jp/ | TogoWS API documentation.TogoWS provides uniformed REST API for accessing major bioinformatics data resources and data formats. |
| 5 | UniChem | https://www.ebi.ac.uk/unichem/ | UniChem efficiently produces cross-references between chemical structure identifiers from different databases. |
| 6 | DrugBank | https://www.drugbank.ca/ | The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information. |
| 7 | Chembl | https://www.ebi.ac.uk/chembl/ | ChEMBL is a manually curated database of bioactive molecules with drug-like properties. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs. |
| 8 | LiverTox | http://www.livertox.nih.gov/ | LiverTox, a National Institues of Health (NIH) web site, provides up-to-date, accurate, and easily accessed information on the diagnosis, cause, frequency, patterns, and management of liver injury attributable to prescription and nonprescription medications, herbals and dietary supplements. |
| 9 | ClinicalTrials.gov | https://clinicaltrials.gov/ | ClinicalTrials.gov is a database of privately and publicly funded clinical studies conducted around the world. |
| 10 | AACT(Access to Aggregate Content of ClinicalTrials.gov) | https://aact.ctti-clinicaltrials.org/ | AACT is a publicly available relational database that contains all information (protocol and result data elements) about every study registered in ClinicalTrials.gov. Content is downloaded from ClinicalTrials.gov daily and loaded into AACT. |
| 11 | CDC(Centers for disease control and prevention) | https://www.cdc.gov/ | CDC works 24/7 to protect America from health, safety and security threats, both foreign and in the U.S. |
| 12 | Health Canada | https://www.canada.ca/en/health-canada.html | Health Canada is responsible for helping Canadians maintain and improve their health. It ensures that high-quality health services are accessible, and works to reduce health risks. |
| 13 | EMA(The European Medicines Agency) | https://www.ema.europa.eu/en | The European Medicines Agency (EMA) is a decentralised agency of the European Union (EU) responsible for the scientific evaluation, supervision and safety monitoring of medicines in the EU. |
| 14 | CTD(Comparative Toxicogenomics Database) | http://ctdbase.org/;jsessionid=004F0FF9F478AC5C6B218EC44E012910 | CTD is a robust, publicly available database that aims to advance understanding about how environmental exposures affect human health. |
| 15 | BRD(The Biospecimen Research Database) | https://brd.nci.nih.gov/brd/ | The BRD is a free and publicly accessible database that contains peer-reviewed primary and review articles as well as SOPs in the field of human Biospecimen Science. |
Popular resource
- GSA: We used the summarized keywords to retrieve the corresponding histological data in NCBI's GEO database (https://www.ncbi.nlm.nih.gov/gds), which was summarized and organized according to the information obtained.
- Device: We compiled how to make Organs-on- chips device including chip material, size, design, processing and surface modification by reading related literature.
- Organs: We searched PubMed(https://pubmed.ncbi.nlm.nih.gov/) for organ-on-a-chip literature related to organs and downloaded the open-access parts of it. The parts that are not open access provide partial information such as abstracts and links.
- Cancer Research: We searched PubMed(https://pubmed.ncbi.nlm.nih.gov/) for organ-on-a-chip literature related to cancer and downloaded the open-access parts of it. The parts that are not open access provide partial information such as abstracts and links.
- DrugBank: We followed the instructions of DrugBank (https://go.drugbank.com/) to download the content that was open access and provided links to the original website for those that were not.
- Patent: We search for relevant data in Google Patents(https://patents.glgoo.top/) using designed keywords, and download and access the open-access part of it.
- Chemicals: We obtained the relevant compound information from Chembl (https://www.ebi.ac.uk/chembl/), all in strict accordance with the website instructions.
- Toxicants: We obtained information on open access toxicants associated with organoids from the Comparative Toxicogenomics Database (http://ctdbase.org/) and correlated it with the literature.
Privacy and Security Policy
- Disclosure: OOCDB does not disclose, give, sell, or transfer any personal information about our visitors, unless required for law enforcement or by statute.
- Personally Identifiable Information (PII): OOCDB hopes to create an accessible communication community that contributes to scientific research. When you visit the OOCDB websites, we do not collect any personally identifiable information (PII) about you, unless you choose to explicitly provide it to us (for example, submit your own data). The OOCDB does not collect information for commercial marketing or any purpose unrelated to OOCDB's Mission.
- What Type of Information OOCDB Collects: We don’t collect any type of information from visitors.
- How to Opt Out or Disable Cookies: If you do not wish to have session or persistent cookies placed on your computer, you can disable them using your Web browser. If you opt out of cookies, you will still have access to all information and resources the OOCDB website provides.
- Copyright Status: Files and files on the OOCDB web server can be downloaded and copied for free. Unlike traditional media repositories, OOCDB shares are free. Everyone is free to copy, use any document here, as long as they follow the terms specified by the author; this usually means properly attributing the source and author, and releasing copies/improvements to others with the same freedom. The license conditions for each media file can be found on its description page. The Organ on a Chip Database (OOCDB) itself and the text within it are licensed under the Creative Commons Attribution/Share Alike License (https://creativecommons.org/licenses/by-sa/3.0/).
Disclaimers
- Liability: For documents and software available from this server, OOCDB does not warrant or assume any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed.
- Endorsement: OOCDB does not endorse or recommend any commercial products, processes, or services. The views and opinions of authors expressed on OOCDB's Web sites do not necessarily state or reflect those of the Southeast University, and they may not be used for advertising or product endorsement purposes.
- External Links: Some OOCDB Web pages provide links to other Internet sites for the convenience of users. OOCDB is not responsible for the availability or content of these external sites, nor does OOCDB endorse, warrant, or guarantee the products, services, or information described or offered at these other Internet sites. Users cannot assume that the external sites will abide by the same Privacy Policy to which OOCDB adheres. It is the responsibility of the user to examine the copyright and licensing restrictions of linked pages and to secure all necessary permissions.
- Medical Information: It is not the intention of OOCDB to provide specific medical advice, but rather to provide users with information to better understand health and disease. Specific medical advice will not be provided, and OOCDB urges you to consult with a qualified health professional for diagnosis and for answers to your personal medical questions.
Overview of the OOCDB
Database Background
In order to establish shared technical specifications and standards, improve the utilization level of organ chip big data, promote organ chip big data mining, and provide an important guarantee for biomedical technology innovation and rapid industrial development. We designed Organ Chip Database (OOCDB) of Southeast University. This database is mainly used for the storage、access and sharing of organ chip scientific data, including: cell tissue organ database、organ chip device database、drug compound library、Organ chip experiment database and user and platform database.
Study components
| Component | Description |
|---|---|
| Assay Method | Assay methods are used to measure assay targets. |
| Assay Targets | Assay targets are used to assess the response of a OOCDB model. |
| Cell Samples | Cell samples are used in OOCDB models . The cell types and cell origins are included as part of the cell sample. |
| Compounds | Chemicals are used in studies and/or features of the OOCDB. Chemical properties are curated from reference sources. |
| Devices | Devices used in OOCDB models with the option to click on the device to view the detail of the device. |
| Diseases | Diseases are added into the OOCDB. |
| Locations | Locations that can be added or removed within the device. |
| Models | Models in OOCDB with the option to click on the model and view the detail of the model's design. |
| Settings | Settings are used to describe the study design. |
| Other Components | Options to view additional components of a study are under development. |
Study Data Organization
| Component | Description |
|---|---|
| Study | A study is a container for all data and metadata associated to an experiment designed to assess OOCDB model response. |
| Matrices | Matrices used to group models within a study. |
| Matrix Items | Matrix items are the generic term for an individual OOCDB model. |
| Assay Images & Videos | Images and videos are attached to a matrix item and displayed within a study. |
Data Sources
| Source# | Data Sources | External Links | Description |
|---|---|---|---|
| 1 | PubMed | https://pubmed.ncbi.nlm.nih.gov/ | PubMed® comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. |
| 2 | Fda(food and drug administration) | https://www.fda.gov/ | The FDA provides information gathered from press releases and other public notices about certain recalls of FDA-regulated products. Not all recalls have press releases or are posted on this website. |
| 3 | PubChem | https://pubchem.ncbi.nlm.nih.gov/ | PubChem is an open chemistry database at the National Institutes of Health (NIH). |
| 4 | TogoWS | http://togows.dbcls.jp/ | TogoWS API documentation.TogoWS provides uniformed REST API for accessing major bioinformatics data resources and data formats. |
| 5 | UniChem | https://www.ebi.ac.uk/unichem/ | UniChem efficiently produces cross-references between chemical structure identifiers from different databases. |
| 6 | DrugBank | https://www.drugbank.ca/ | The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information. |
| 7 | Chembl | https://www.ebi.ac.uk/chembl/ | ChEMBL is a manually curated database of bioactive molecules with drug-like properties. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs. |
| 8 | LiverTox | http://www.livertox.nih.gov/ | LiverTox, a National Institues of Health (NIH) web site, provides up-to-date, accurate, and easily accessed information on the diagnosis, cause, frequency, patterns, and management of liver injury attributable to prescription and nonprescription medications, herbals and dietary supplements. |
| 9 | ClinicalTrials.gov | https://clinicaltrials.gov/ | ClinicalTrials.gov is a database of privately and publicly funded clinical studies conducted around the world. |
| 10 | AACT(Access to Aggregate Content of ClinicalTrials.gov) | https://aact.ctti-clinicaltrials.org/ | AACT is a publicly available relational database that contains all information (protocol and result data elements) about every study registered in ClinicalTrials.gov. Content is downloaded from ClinicalTrials.gov daily and loaded into AACT. |
| 11 | CDC(Centers for disease control and prevention) | https://www.cdc.gov/ | CDC works 24/7 to protect America from health, safety and security threats, both foreign and in the U.S. |
| 12 | Health Canada | https://www.canada.ca/en/health-canada.html | Health Canada is responsible for helping Canadians maintain and improve their health. It ensures that high-quality health services are accessible, and works to reduce health risks. |
| 13 | EMA(The European Medicines Agency) | https://www.ema.europa.eu/en | The European Medicines Agency (EMA) is a decentralised agency of the European Union (EU) responsible for the scientific evaluation, supervision and safety monitoring of medicines in the EU. |
| 14 | CTD(Comparative Toxicogenomics Database) | http://ctdbase.org/;jsessionid=004F0FF9F478AC5C6B218EC44E012910 | CTD is a robust, publicly available database that aims to advance understanding about how environmental exposures affect human health. |
| 15 | BRD(The Biospecimen Research Database) | https://brd.nci.nih.gov/brd/ | The BRD is a free and publicly accessible database that contains peer-reviewed primary and review articles as well as SOPs in the field of human Biospecimen Science. |
Recording Videos Demostrating Database Features
Instroduction of the Organ Chip Database (OOCDB)
Database
GSA
Device
Organs
Cancer Research
DrugBank
Patent
Chemcial
Toxnet
Brain Science
Featured Resources
Featured Resources
Organ on a chip study
Mathematical modeling
Brain on a chip
Standardization
Submission
Database Features
Instroduction of the Organ Chip Database (OOCDB)
Welcome to organ chip database. OCbd is a unified platform that provides organ chip biological big data sharing and application services for scientific research communities. OCbd mainly includes Popular resources and Featured resources. This database is open resource for all academic researchers and we also highly welcome you to join us and share your data and experiences.
Database
- 1. GSA: GSA collects and organizes the raw data of organ chip, and show the organ classification chart and number trend with the year.
- 2. Device: Device show how to make Organs-on- chips device including chip material, size, design, processing and surface modification.
- 3. Organs: Organs collects and organizes literature about organ chips，and provides common indicators and organ indexes to search.
- 4. Cancer research: Cancer research shows the literature about organ chips, and provides common indicators and organ index to search.
- 5. DrugBank: DrugBank shows the common drugs based on organ chips, the basic information, and the chemical structure. Drug entry links the original source.
- 6. Patent: Patent collects and organizes patents from different countries related to Organs-on- chips, and provides expire date and country to search. Click export patent to download patent data.
- 7. Chemicals: Chemicals shows the basic information of chemicals based on organ chips.
- 8. Toxicants: Toxicants Database shows the toxic based on organ chips, and provides different indexes to search.
Brain Science
Brain science collects and organizes literature about brain research, and provides different indexes to search.
Featured Resources
- 1. Featured resource: OOCDB provides four featured resource based on organ on chips including Organ on a Chip Study、Mathematical modeling、Brain on a Chip and Standardization.
- 2. Organ on a Chip Study: Organ on a Chip Study show the x-ray human brain anatomy with inner structure and torso medically accurate high-quality 3D model.
- 3. Mathematical modeling: Mathematical modeling provides tissue enrichment analysis，you can compare to the standard datasets in this database or customer provided datasets.
- 4. Brain on a Chip: Brain on a Chip show the distribution map of national patents、academic paper trends and the latest academic information related to brain research.
- 5. Standardization: Standardization provides four standardizations including Standardization of Organ Chip Device 、Standardization of Organ Chip Experimental Procedure、Standardization of Organ Chip Data Analysis、Standardization of Organ Chip Data Format.
Submission
You can register an account to join us and share your data and experiences.
BBS
You can post online to share your experiences or communicate with other users.
Searching the OOCDB
Global Search
Use a Global Search to search the whole OOCDB from the Home page
- Go to the OOCDB Home page
- Type search text in the Search bar
- Click the Search button
Advanced Search
Use Advanced Search to search the whole OOCDB from the Home page
- Go to the OOCDB Home page
- Click Advanced Search which is under the Search bar
- Select a database (Literature、Drug、GSA、Patent)
- Choose criteria and enter a keyword
- Click “+” or “-” to add or subtract criteria
- Click the Search button below
Search and Sorts List
There are many places in the database where searches can be made with search bars located at the top
- Choose different indexes
- Type a search term in the search bar
- Click the Search button linked to be routed to desired location
Indexes include the following
- Expired date and Country in Patent
- Common indicators and Organ index in Cancer Research and Organs
- Filter of different organs and tissues in GSA (including All、adrenal gland、articulation 、bile、bladder、blood vessel、bone、brain、ear、esophagus、eye、genital system 、heart、kidney、liver、lung、muscle、nervous system 、pancreas、prostate、rectum 、reproductive system、skeleton 、soft tissue、spleen、stomach、thymus、Thyroid)
- Sixteen database indicators in Toxicants
Common indicators include the following
- Sources of cells
- Types of cells
- Protein expression level
- Phase contrast image
- DIC image
- Fluorescence image
Organ index include the following
- Heart chip
- Liver chip
- Vascular chip
- Skin chip
- Lung chip
- Intestinal chip
- Neural chip
- Tumor chip
- Reproductive System and Embryo Chip
Sixteen database indicators include the following
- Disease vocabulary (MEDIC)
- Pathway vocabulary
- Chemical vocabulary
- Chemical-pathway enriched associations
- Chemical- -GO enriched associations
- Chemical- -gene interactions
- Chemical- -disease associations
- Chemical- -gene interaction types
- Exposure- -event associations
- Exposure- -study associations
- Phenotype (GO) - Disease Inference Networks
- Gene vocabulary
- Disease- -pathway associations
- Chemical- -phenotype interactions
- Gene- -pathway associations
- Gene- -disease associations
Instructions for Data Providers
Step1
Describe your research clearly and concisely, including the research name、type,、abstract、start time and model name used. You can paste in the text area or select a file (Word or PDF) to upload.
Step2
Submit your personal information in the box below, mainly including your name、organization/company and email.
Step3
Complete other information about your research、the type of organ or cell and the model of the device. We also need you to upload a device description or picture.
Step4
Fill in drug or toxicant、publication and patent of the research if any.