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The Digital Ageing Atlas: integrating the diversity of age-related changes into a unified resource.

Craig T, Smelick C, Tacutu R, Wuttke D, Wood SH, Stanley H, Janssens G, Savitskaya E, Moskalev A, Arking R, de Magalhães JP - Nucleic Acids Res. (2014)

Bottom Line: Currently, researchers must consult several sources, including primary publications, in order to obtain age-related data at various levels.In addition, we developed an intuitive and user-friendly interface that allows searching, browsing and retrieving information in an integrated and interactive fashion.Overall, the DAA offers a new approach to systemizing ageing resources, providing a manually-curated and readily accessible source of age-related changes.

View Article: PubMed Central - PubMed

Affiliation: Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK.

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Related in: MedlinePlus

A labelled diagram of the entry for IGF1 age-related changes in the plasma: (1) Each change is colour coded for easy identification of type. (2) As all changes are assigned to a tissue it is easy to see the different changes occurring on an organ level. (3) Each change is fully referenced allowing for additional details into the methodology and access to the original data. (4) Clear identification of the amount and direction of change with age (if applicable) is provided, along with how it was derived. (5) Changes can be stored persistently between sessions as well as compared on-site using the graphing functionality. (6) Descriptions provide more details, including greater clarification regarding the context in which the change was observed and/or measured. (7) Linking changes to genes allows, much like linking tissues, the ability to see all the changes associated with a particular gene.
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Figure 2: A labelled diagram of the entry for IGF1 age-related changes in the plasma: (1) Each change is colour coded for easy identification of type. (2) As all changes are assigned to a tissue it is easy to see the different changes occurring on an organ level. (3) Each change is fully referenced allowing for additional details into the methodology and access to the original data. (4) Clear identification of the amount and direction of change with age (if applicable) is provided, along with how it was derived. (5) Changes can be stored persistently between sessions as well as compared on-site using the graphing functionality. (6) Descriptions provide more details, including greater clarification regarding the context in which the change was observed and/or measured. (7) Linking changes to genes allows, much like linking tissues, the ability to see all the changes associated with a particular gene.

Mentions: Each age-related change in the DAA has its own page displaying a variety of information. Typically, entries include a description of the change with age, a quantification (if available) of the change with age (e.g. a percentage gene expression change between two ages), at least one reference and relevant links (Figure 2). The way in which the changes are stored in the database is best described in an object-orientated way. The key objects in the DAA are change, tissue, gene, property and data. The change object stores the basic information on a change including type, age of occurrence, gender (if available) and organism. The gene object contains basic information on a gene, e.g. symbol and name, mapping to other information such as homologues in other organisms, Gene Ontology (GO) terms and links to external resources, for instance cross-linking to the GenAge database of ageing-related genes (12) (Figure 3). Gene information can then be associated with multiple changes to prevent repetition and ensure ease of updating when elements such as the gene symbol change. It also allows for the DAA to display all changes associated with a gene making it easier to find information. The tissue object contains details on a tissue such as a name and description. The tissue objects (currently 284 different tissues are represented) are arranged into a simple hierarchical structure, based upon the ontology created by eVOContology (13), supplemented by descriptive data from both Brenda (14) and Wikipedia (http://en.wikipedia.org) and further expanded in our lab. Each tissue has a parent and zero or more children. The root parent represents the whole organism and the tissue hierarchy can be navigated on our interface. Each change is associated with one or more tissues, allowing for exploration of the number and types of changes occurring in each tissue or organ.


The Digital Ageing Atlas: integrating the diversity of age-related changes into a unified resource.

Craig T, Smelick C, Tacutu R, Wuttke D, Wood SH, Stanley H, Janssens G, Savitskaya E, Moskalev A, Arking R, de Magalhães JP - Nucleic Acids Res. (2014)

A labelled diagram of the entry for IGF1 age-related changes in the plasma: (1) Each change is colour coded for easy identification of type. (2) As all changes are assigned to a tissue it is easy to see the different changes occurring on an organ level. (3) Each change is fully referenced allowing for additional details into the methodology and access to the original data. (4) Clear identification of the amount and direction of change with age (if applicable) is provided, along with how it was derived. (5) Changes can be stored persistently between sessions as well as compared on-site using the graphing functionality. (6) Descriptions provide more details, including greater clarification regarding the context in which the change was observed and/or measured. (7) Linking changes to genes allows, much like linking tissues, the ability to see all the changes associated with a particular gene.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384002&req=5

Figure 2: A labelled diagram of the entry for IGF1 age-related changes in the plasma: (1) Each change is colour coded for easy identification of type. (2) As all changes are assigned to a tissue it is easy to see the different changes occurring on an organ level. (3) Each change is fully referenced allowing for additional details into the methodology and access to the original data. (4) Clear identification of the amount and direction of change with age (if applicable) is provided, along with how it was derived. (5) Changes can be stored persistently between sessions as well as compared on-site using the graphing functionality. (6) Descriptions provide more details, including greater clarification regarding the context in which the change was observed and/or measured. (7) Linking changes to genes allows, much like linking tissues, the ability to see all the changes associated with a particular gene.
Mentions: Each age-related change in the DAA has its own page displaying a variety of information. Typically, entries include a description of the change with age, a quantification (if available) of the change with age (e.g. a percentage gene expression change between two ages), at least one reference and relevant links (Figure 2). The way in which the changes are stored in the database is best described in an object-orientated way. The key objects in the DAA are change, tissue, gene, property and data. The change object stores the basic information on a change including type, age of occurrence, gender (if available) and organism. The gene object contains basic information on a gene, e.g. symbol and name, mapping to other information such as homologues in other organisms, Gene Ontology (GO) terms and links to external resources, for instance cross-linking to the GenAge database of ageing-related genes (12) (Figure 3). Gene information can then be associated with multiple changes to prevent repetition and ensure ease of updating when elements such as the gene symbol change. It also allows for the DAA to display all changes associated with a gene making it easier to find information. The tissue object contains details on a tissue such as a name and description. The tissue objects (currently 284 different tissues are represented) are arranged into a simple hierarchical structure, based upon the ontology created by eVOContology (13), supplemented by descriptive data from both Brenda (14) and Wikipedia (http://en.wikipedia.org) and further expanded in our lab. Each tissue has a parent and zero or more children. The root parent represents the whole organism and the tissue hierarchy can be navigated on our interface. Each change is associated with one or more tissues, allowing for exploration of the number and types of changes occurring in each tissue or organ.

Bottom Line: Currently, researchers must consult several sources, including primary publications, in order to obtain age-related data at various levels.In addition, we developed an intuitive and user-friendly interface that allows searching, browsing and retrieving information in an integrated and interactive fashion.Overall, the DAA offers a new approach to systemizing ageing resources, providing a manually-curated and readily accessible source of age-related changes.

View Article: PubMed Central - PubMed

Affiliation: Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK.

Show MeSH
Related in: MedlinePlus