The Comparative Toxicogenomics Database - Revision history

Kwrigh35: Added link to presentation

2017-10-03T07:11:07Z

Added link to presentation

Kwrigh35: /* Electronic Notebook */ added information about the technology that runs CTD

2017-10-02T23:29:50Z

‎Electronic Notebook: added information about the technology that runs CTD

Kwrigh35: /* Summary Judgement */ added answer for #2

2017-10-02T23:17:15Z

‎Summary Judgement: added answer for #2

Kwrigh35: /* General Utility */ fixed capital letters. re-worded a couple of sentences. Added image about data browsing.

2017-10-02T23:07:52Z

‎General Utility: fixed capital letters. re-worded a couple of sentences. Added image about data browsing.

Kwrigh35: /* General Utility */ Edited answer for question 2.

2017-10-02T20:01:25Z

‎General Utility: Edited answer for question 2.

Kwrigh35: /* Acknowledgements */ added a line break between signatures

2017-10-02T00:12:50Z

‎Acknowledgements: added a line break between signatures

Zvanysse at 00:12, 2 October 2017

2017-10-02T00:12:11Z

Kwrigh35: /* Acknowledgements */ added acknowledgements and signature

2017-10-02T00:11:28Z

‎Acknowledgements: added acknowledgements and signature

Zvanysse: hyperlinked webpages in general utility

2017-10-02T00:09:41Z

hyperlinked webpages in general utility

Kwrigh35: added Zach's template

2017-10-01T23:59:35Z

added Zach's template

@@ Line 65: / Line 65: @@
 *Overall, we learned about how CTD goes about curating, storing, and organizing their data. It seems like CTD was aware of the complexity of the field, so they tried to make it as user-friendly as they could, without changing the primary focus for the database. CTD has around 35 million manually curated data that has been well preserved and readily available for public use.
 *While not part of the assignment, we found information about the [http://ctdbase.org/help/faq/;jsessionid=3CC4EFABDAA72A9CC9A5C89589335E71?p=6422645 technology that runs CTD].  We thought that it was really interesting that most of the software and services used by the database are open source.  This is another example of why supporting open source computing is important; it allows projects like CTD become reality without as many prohibitive costs.
 ==Acknowledgements==

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 *On Sunday, October 1, we met with the goal to finish this assignment page as well as the presentation. We were able to complete most of the assignement. as we just had to tweak and fine tune some of the specifications.
 *Overall, we learned about how CTD goes about curating, storing, and organizing their data. It seems like CTD was aware of the complexity of the field, so they tried to make it as user-friendly as they could, without changing the primary focus for the database. CTD has around 35 million manually curated data that has been well preserved and readily available for public use.
 ==Acknowledgements==

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 ==Summary Judgement==
 #As an inexperienced user who has very little knowledge about comparative toxicogenomics, I would not recommend this database to them. I believe that there should be some knowledge about the field beforehand before utilizing the database. For me personally, I do not know how I would use this information for my personal benefit other than appreciation for the field.
 ==Electronic Notebook==

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 #*[https://www.ncbi.nlm.nih.gov/taxonomy NCBI Taxonomy] (as of August 18, 2017)
 #*[https://www.ncbi.nlm.nih.gov/pubmed PubMed®] (as of August 18, 2017)
-#*[http://reactome.org/ Reactome] (as of August 18, 2017) <p> Links to PubMed are also sprinkled throughout the database, particularly as links to the specific scientific article page that a piece of datum comes from. </p>
+#*[http://reactome.org/ Reactome] (as of August 18, 2017) <p> Links to PubMed are also sprinkled throughout the database, particularly as links to the specific scientific article page that a piece of datum comes from. </p> [[File:CTD_Data_Browsing.JPG|750px|thumb|right|This figure shows three pathways that one can take while browsing in order to get to the page with data on Ascorbic Acid.  The pathway highlighted in the red box is the one we took to Ascorbic Acid.]]
 #Browsing the data isn't particularly difficult, but neither is it particularly easy. The browsing experience really depends on the type of data you are looking for.  There are several categories of data, but within each category the browsing capability changes.
-#*In the gene category, there is no way to filter the data; genes are simply listed alphabetically. Finding a gene this way is virtually useless because of the sheer amount of data. Overall, It is much easier to find data by performing a broad search with a few well thought out parameters, and then browse the results. Conducting a search that casts a wide net makes the data much more manageable.
+#*In the gene category, there is no way to filter the data; genes are simply listed alphabetically. Finding a gene this way is quite tedious due to the sheer amount of data. To find data, it is much easier to perform a broad search (with a few well thought out parameters) and then browse the results. Conducting a search that casts a wide net makes the data much more manageable.
-#*For information on Exposure studies, no browsing is available.
+#*For information on exposure studies, no browsing is available.
 #*Data browsing is only convenient for chemicals or diseases.  The database provides a navigational list of chemical/disease categories that become more narrow with each click. For example, I was able to find information on different variations of Ascorbic Acid quite easily, since I knew it was an acidic sugar. [[File:CTD_Download_Example.jpg|800px|thumb|right|Links to download data spreadsheets are at the bottom of each page.  In this image they are highlighted by a red box.]]
 #Yes, downloading data is convenient. For example, one can download the table of diseases associated with gene [http://ctdbase.org/detail.go?type=gene&acc=189099&view=disease W02A2.8] in several file formats. CSV, Excel, XML, and TSV files are all available to download, allowing users to choose whichever file format will work best with their favorite software. While making a specific query, data can also be downloaded in any of the following standard formats: TSV, CSV, JSON, or XML.

@@ Line 48: / Line 48: @@
 #*[https://www.ncbi.nlm.nih.gov/pubmed PubMed®] (as of August 18, 2017)
 #*[http://reactome.org/ Reactome] (as of August 18, 2017) <p> Links to PubMed are also sprinkled throughout the database, particularly as links to the specific scientific article page that a piece of datum comes from. </p>
-#Browsing the data isn't particularly difficult, but neither is it particularly easy. One of the reasons why it is difficult to browse CTD is because of the sheer amount of data it contains. There are very few ways to filter the data when browsing.  It is much easier to find data by performing a broad search with a few well thought out parameters, and then browse the results. Conducting a search that casts a wide net makes the data much more manageable.   [[File:CTD_Download_Example.jpg|800px|thumb|right|Links to download data spreadsheets are at the bottom of each page.  In this image they are highlighted by a red box.]]
+#Browsing the data isn't particularly difficult, but neither is it particularly easy. The browsing experience really depends on the type of data you are looking for.  There are several categories of data, but within each category the browsing capability changes.
 #Yes, downloading data is convenient. For example, one can download the table of diseases associated with gene [http://ctdbase.org/detail.go?type=gene&acc=189099&view=disease W02A2.8] in several file formats. CSV, Excel, XML, and TSV files are all available to download, allowing users to choose whichever file format will work best with their favorite software. While making a specific query, data can also be downloaded in any of the following standard formats: TSV, CSV, JSON, or XML.
 #Yes, the database is very user-friendly, the database utilizes a broad to specific design. The user is able to click on legend icons for quick help. On the homepage, a clickable image navigates the user to the desired data category. It is very easy to query data, as it is a multi-step process that has "help" notifications the whole way. If a user is still confused, there are tutorial videos on how to navigate through the webpage.

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 *While we worked with the people noted above, this journal entry was completed by Zach and Katie and not copied from another source.
-[[User:Kwrigh35|Kwrigh35]] ([[User talk:Kwrigh35|talk]]) 17:11, 1 October 2017 (PDT)
+[[User:Kwrigh35|Kwrigh35]] ([[User talk:Kwrigh35|talk]]) 17:11, 1 October 2017 (PDT) <br>
 [[User:Zvanysse|Zvanysse]] ([[User talk:Zvanysse|talk]]) 17:12, 1 October 2017 (PDT)

← Older revision		Revision as of 00:12, 2 October 2017
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	[[User:Kwrigh35\|Kwrigh35]] ([[User talk:Kwrigh35\|talk]]) 17:11, 1 October 2017 (PDT)		[[User:Kwrigh35\|Kwrigh35]] ([[User talk:Kwrigh35\|talk]]) 17:11, 1 October 2017 (PDT)
		+	[[User:Zvanysse\|Zvanysse]] ([[User talk:Zvanysse\|talk]]) 17:12, 1 October 2017 (PDT)

	==References==		==References==

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 ==Acknowledgements==
-*We acknowledge working on the assignment together
+*[[User:Zvanysse| Zach]] and [[User:Kwrigh35| Katie]] would like to thank each other for being good homework partners.  We met in the afternoon on Friday and Sunday to write this wiki page and our presentation slides.  We also plan on meeting Monday to rehearse our presentation.
 ==References==

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 ==General Utility==
 #Links to the following databases can be found on the CTD [http://ctdbase.org/about/dataStatus.go Data Status] page:
-#*BioGRID (3.4.151 release)
+#*[https://thebiogrid.org/ BioGRID] (3.4.151 release)
-#*ChemIDplus® (as of August 18, 2017)
+#*[https://chem.nlm.nih.gov/chemidplus/ ChemIDplus®] (as of August 18, 2017)
-#*DrugBank (as of August 18, 2017)
+#*[https://www.drugbank.ca/ DrugBank] (as of August 18, 2017)
-#*GO (as of August 18, 2017)
+#*[http://www.geneontology.org/ GO] (as of August 18, 2017)
-#*KEGG (as of August 18, 2017)
+#*[http://www.genome.jp/kegg/ KEGG] (as of August 18, 2017)
-#*MeSH® (2016 MeSH release)
+#*[https://www.nlm.nih.gov/mesh/meshhome.html MeSH®] (2016 MeSH release)
-#*NCBI Gene (as of August 18, 2017)
+#*[https://www.ncbi.nlm.nih.gov/gene NCBI Gene] (as of August 18, 2017)
-#*NCBI Taxonomy (as of August 18, 2017)
+#*[https://www.ncbi.nlm.nih.gov/taxonomy NCBI Taxonomy] (as of August 18, 2017)
-#*PubMed® (as of August 18, 2017)
+#*[https://www.ncbi.nlm.nih.gov/pubmed PubMed®] (as of August 18, 2017)
-#*Reactome (as of August 18, 2017) <p> Links to PubMed are also sprinkled throughout the database, particularly as links to the specific scientific article page that a piece of datum comes from. </p>
+#*[http://reactome.org/ Reactome] (as of August 18, 2017) <p> Links to PubMed are also sprinkled throughout the database, particularly as links to the specific scientific article page that a piece of datum comes from. </p>
 #Browsing the data isn't particularly difficult, but neither is it particularly easy. One of the reasons why it is difficult to browse CTD is because of the sheer amount of data it contains. There are very few ways to filter the data when browsing.  It is much easier to find data by performing a broad search with a few well thought out parameters, and then browse the results. Conducting a search that casts a wide net makes the data much more manageable.   [[File:CTD_Download_Example.jpg|800px|thumb|right|Links to download data spreadsheets are at the bottom of each page.  In this image they are highlighted by a red box.]]
 #Yes, downloading data is convenient. For example, one can download the table of diseases associated with gene [http://ctdbase.org/detail.go?type=gene&acc=189099&view=disease W02A2.8] in several file formats. CSV, Excel, XML, and TSV files are all available to download, allowing users to choose whichever file format will work best with their favorite software. While making a specific query, data can also be downloaded in any of the following standard formats: TSV, CSV, JSON, or XML.

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