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title: '**PROJECT 1: BIOLOGICAL DATABASES**'

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# **PROJECT 1: BIOLOGICAL DATABASES**
by Shannia Sid De Leon | October 4, 2021
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**Table of Contents**
[TOC]

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## Posed Research Question 
Can we create a reliable method to predict colorectal cancer using a patient's genome and genetic patterns before they show symptoms? 

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## What is Meta?

[Meta](https://www.meta.org/) is an online database containing published papers in the biomedical field and is funded by the [Chan Zuckerberg Initiative Foundation](https://chanzuckerberg.com/science/), a nonprofit private foundation whos mission statement is to "cure, prevent, or manage all diseases by the end of this century" (https://chanzuckerberg.com/science/our-values-approach/). 

==Meta can be used to answer nearly any biological question in the biomedical sciences field. Since it is similar to a search engine like Google Scholar, I believe that it can answer any biomedical question as long as it does not require raw data such as raw DNA sequences.== 


Since we are focusing on colorectal cancer, Meta would perfectly fit our research program's needs. [Meta](https://www.meta.org/) is an online database containing published papers in the biomedical field and is funded by the [Chan Zuckerberg Initiative Foundation](https://chanzuckerberg.com/science/), a nonprofit private foundation who's mission is to "cure, prevent, or manage all diseases by the end of this century". Since we are focusing on colorectal cancer, Meta would perfectly fit our research program's needs.

 


| ![alt text](https://pbs.twimg.com/profile_images/1294335040038604807/nEB_G5jf.jpg =200x) | ![alt text](https://www.cshl.edu/wp-content/uploads/2017/04/czi_hero.jpg =300x) |
| ---------------------------------------------------------------------------------------- | -

*sources: (1) https://pbs.twimg.com/profile_images/1294335040038604807/nEB_G5jf.jpg , (2) https://www.cshl.edu/wp-content/uploads/2017/04/czi_hero.jpg


### What Makes Meta Different?
The database is similar to other academic search engines such as Google Scholar and PubMed. Meta, however, is different in the way that it tailors personalized feeds for biomedical researchers to get live updates about new research relevant to their specific research interests. 

Creating personalized fields not only allows us to find specific findings, but also to connect concepts and produce new ideas about colorectal cancer. Meta personalizes user feeds by analyzing and clustering millions of public sources in an algorithim to build a living map of science called the "Knowledge Graph". In this Knowledge Graph, we can easily find information by fields such as Authors names, paper titles, date published, etc. 

Users can subscribe to specific areas of research such as genetic disorders, drugs, cell biology, and labs and institutes. For our research purposes, we would begin finding the niche subset of entries about colorectal cancer by subscribing to the topics of colorectal cancers, genetic markers, and colonoscopy.

### Format of Database
This database primarily has secondary characteristics. The site links published work from other datasources like PubMed, Nature Communications, and Crossref. 

### Navigating Meta
A simple search for 'genetics of colorectal cancer' using the Meta search bar generated papers from well known journals such as Journal of Gastroenterology, Genes & Development, and Frontiers in Genetics. Papers are presented in a feed format. Meta also has a feature that hyperlinks entries to discussions on the same topic to other platforms such as Twitter and Mendeley.

| ![image alt](https://pbs.twimg.com/profile_images/624673260047888384/VJ5cIZGu_400x400.jpg =300x) | ![alt text](https://d2y3t9c9501wi7.cloudfront.net/wp-content/uploads/2018/09/8b81bc_e5a2b930a0ba94b6dd967b27b36c8bab.gif) | ![image alt](https://frontiersinblog.files.wordpress.com/2015/08/genetics_290x290.jpg?w=290) |
|:------------------------------------------------------------------------------------------------:| ------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------- |

*sources: 
(1) https://pbs.twimg.com/profile_images/624673260047888384/VJ5cIZGu_400x400.jpg , 
(2) https://d2y3t9c9501wi7.cloudfront.net/wp-content/uploads/2018/09/8b81bc_e5a2b930a0ba94b6dd967b27b36c8bab.gif, 
(3) https://frontiersinblog.files.wordpress.com/2015/08/genetics_290x290.jpg?w=290

  







### Accessibility
Access to Meta is unrestricted and open to anyone on the web, but in order to create a personalized feed the website requires users to create an account. Creating an account is free. To access and read the papers, Meta has hyperlinks to either download a PDF or to outsource to an external database. Entries are labled as to whether or not the papeers are open access or require a subscription or membership to that specific database. These features will make it easier for our researchers to find papers that are open, accessible, and free without the ambiguity that journals with mandated subscriptions sometimes have.

==Data on meta can be accessed computationally using any internet browser==

### Site Maintenance
Other than stating that it relies on public sources, Meta does not state how entries are managed and updated. The site reiterates that the tool is operatetd under the Chan Zuckerburg Initiative Foundation but does not specificy specific names of managers of the site. 

### Licensure and Restrictions
Since all entries on Meta are linked to other sources, there are no specific restrictions specified within the site's privacy and policies. Specific restrictions as to how users can use the data varies from which source each paper comes from. In a way, the issue of licensure and restrictions aren't really applicable as Meta is more of a tool to access data than a site with raw data. 

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## Critical Review of Meta

### Ease of Use
Meta is very simple to navigate, as there is a search bar feature to find what you need. In addition, there are search settings to sort results by relevance, type, concept, method, and date. 

### Quality
From personal exploration of the website, the entries on Meta are from a wide variety of credible and well-known academic journals and databases in science. Papers on Meta are nearly identical to papers on such large databases like PLOS One and Jstor. 

### Room for Improvement
==One aspect that Meta does not have compared to other search engine databases such as [The American Journal of Medicine ](https://www.amjmed.com/)is a homepage. I believe a homepage provides a central page of navigation that contributes to the overall organization and presentation of the database. I think Meta should implement a homepage with sections highlighting current news, an 'about' section describing what Meta is, and prominent hyperlinks to explore outside resources (see example from The American Journal of Medicine below).== 

![](https://i.imgur.com/ySxmosF.png)
**Example of a homepage from The American Journal of Medicine. Hyperlinks are clearly laid out and there is a central page for users to return to.**

*source: (1) https://www.amjmed.com/

==In addition, I think creating an 'about' section giving a description of what exactly Meta is right off the bat on a homepage would allow users to understand the database's purpose much quicker. As of right now, the only way to access the description that  Meta is a tool for biomedical researchers is by clicking on the small 'help' hyperlink on the bottom left of the page that takes you to the help center where you have to further click on 'Overview' > 'Meta Overview' > 'What is Meta' to finally access the description. This is too complicated of a navigation just to find a description, and could be more direct by creating a homepage with an 'about' section.==


### Suggestion to Implement Social Media Aspect
I think Meta can enhance the social aspect of their platform by enabling features similar to Facebook Groups, where researchers can join specific groups catered to their niche topics. I think this would add another layer of specificity to the site. 

Another flaw I notice on the site is the inability for users to interact with one another. I think implementing a comments section with thread features would stimulate discussion among the researchers about each entry. This would be helpful to researchers like us because it would enable to bounce ideas off of eachother as well as remain critical of published data. Another layer to promote interpersonal discussions would be to create a direct messaging feature for more private conversations. This would be particularly be beneficial in researching our own research question because we can connect to renowned labs or institutions knowledgable in the genetics of colorectal cancer. 

To improve transparency and credibility, I think another improvement is to have a feature that indicates who has uploaded each entry, and the names of the managers responsible for monitoring the entries. 

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## Conclusion


Overall, I believe Meta will allow our research group to easily stay up-to-date on real-time findings on the genetic trends of colorectal cancer. I personally believe that the website can further by improved by implementing social features such as direct messaging, comments and threads, and interest groups, as this would stimulate more ideas and insights amongst our peers also studying colorectal cancer. 

Nonetheless, this research tool will allow us to navigate and monitor through papers relevant to colorectal genetic discoveries more conveniently. 