Change - The Lifespan App

Created on Aug. 29, 2012, 1:26 p.m. by Hevok & updated on Oct. 26, 2012, 10:58 a.m. by Hevok

The lifespan app aims to systemically cartography all lifespan affecting factors. It is logical structured as follows:


First of all we need to identify all the studies reporting lifespan experiments. The best-developed portal to the biomedical literature is provided by NCBI Entrez as so called PubMed. To aging relevant articles can easily be found via simple Boolean combinations of keywords:

(aging OR ageing) AND (longevity OR lifespan OR life-span OR (life span))

Or it can for instance be further narrowed down to the modulation of the aging process by diet:

(aging OR ageing OR lifespan OR longevity OR (life span) OR (life-span)) AND restriction AND (caloric OR calorie OR dietary OR energy OR (amino acids) OR methionine OR food OR sugar)

You can try your own Boolean combinations to see if you are able narrow down a search to the most for you interesting articles without losing too much relevant ones. It is like applying a filter but keep in mind that there is always a trait-off adding keywords and removing ones. The above two are fairly optimized to filter on lifespan relevant information in general.

You can browse the titles of the list and get a first impression on what happened in the last time in this field.

If a title sounds amazing then click on it to see a small summary of the article called abstract and maybe already some figures. If the abstract indicate that it contains useful information such as lifespan experiments then check out if there is the right top a symbol which indicates whether and where the full text article can be obtained.

Make sure that the article contains lifespan data such as lifespan curves or tables. Sometimes this is already obvious from the abstract and and figures seen in PubMed.

If it is the case we can check out whether the article and its information is already in Denigma. In the Admin of the Lifespan app we go to Studies and paste in either the title or the PubMed ID (which is a integer number found below the abstract in PubMed) and save it. You can also provide a link to the full text article in the field "link" which helps to get to the article as quickly as possible. if the lifespan study is not yet known to Denigma no exception will be raised.


Now we are going to add the lifespan Experiments. Create an experiment for each table and figure which provides lifespan data and associate it with the correct study and species. Use the figure or table title as the name for an experiments series. Include the lifespan data into the data field.

For a table just copy and paste the table and adjust the header to match the columns with adequate descriptions. Individual rows should be separated by either space or tab '/t'. Use tabs if the spaces are themselves used in any columns such as in multi-word terms. Otherwise spaces are preferred.

In the case of a figure we can read the required data from the lifespan curve with the help of a ruler.

Make sure that there is an empty line between header and the data itself.

Save the experiments which will be processed automatically for you.

Tags: tutorial
Categories: Tutorial
Parent: Tutorials Overview

Comment: Updated entry

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