The Monarch Initiative - Revision history

Nicolekalcic: added heading

2017-10-03T07:17:57Z

added heading

Dbashour: updated references

2017-10-03T07:14:23Z

updated references

Nicolekalcic: added submission

2017-10-03T07:13:31Z

added submission

Dbashour: syntax fix

2017-10-03T05:56:30Z

syntax fix

Dbashour: changed source information

2017-10-03T05:55:48Z

changed source information

Dbashour: added electronic notebook

2017-10-03T04:30:16Z

added electronic notebook

Dbashour: syntax fix

2017-10-03T04:18:41Z

syntax fix

Dbashour: edited syntax

2017-10-03T04:18:02Z

edited syntax

Dbashour: edited syntax

2017-10-03T04:17:20Z

edited syntax

Dbashour: edited information

2017-10-03T02:05:27Z

edited information

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-This is [[User:Nicolekalcic|Nicole Kalcic]]'s and [[User:Dbashour|Dina Bashour]]'s [[Week 5]] assignment.
+This is [[User:Nicolekalcic|Nicole Kalcic]]'s and [[User:Dbashour|Dina Bashoura]]'s [[Week 5]] assignment.
-To begin, we found our database by browsing the information via [https://academic.oup.com/nar/article/45/D1/D1/2770636/The-24th-annual-Nucleic-Acids-Research-database Descriptions of new online databases in the 2017 NAR Database issue]. After settling on [https://monarchinitiative.org The Monarch Initiative], we split up the questions below. [[User:Nicolekalcic|Nicole Kalcic]] completed the first and second bolded sections. [[User:Dbashour|Dina Bashour]] completed the second and fourth bolded sections. The finished assignment was checked by both of us to insure there were no mistakes in our own sections or the other person's sections.
+To begin, we found our database by browsing the information via [https://academic.oup.com/nar/article/45/D1/D1/2770636/The-24th-annual-Nucleic-Acids-Research-database Descriptions of new online databases in the 2017 NAR Database issue]. After settling on [https://monarchinitiative.org The Monarch Initiative], we split up the questions below. [[User:Nicolekalcic|Nicole Kalcic]] completed the first and second bolded sections. [[User:Dbashour|Dina Bashoura]] completed the second and fourth bolded sections. The finished assignment was checked by both of us to insure there were no mistakes in our own sections or the other person's sections.
 * '''General information about the database'''
 # Link to the database: https://monarchinitiative.org
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 ==Submission==
+[[File:The Monarch Initiative.pdf]]
 ==Electronic Notebook==
@@ Line 41: / Line 42: @@
 ==Acknowledgements==
-* [[User:Nicolekalcic|Nicole Kalcic]] and [[User:Dbashour|Dina Bashour]] communicated via text and met in person to complete the different requirements of this assignment.
+* [[User:Nicolekalcic|Nicole Kalcic]] and [[User:Dbashour|Dina Bashoura]] communicated via text and met in person to complete the different requirements of this assignment.
 * We looked at the formatting of the [[MiRPathDB Week 5|MiRPathDB]] page in order to help construct ours.
 * While we worked with the people noted above, this individual journal entry was completed by us and not copied from another source.

@@ Line 52: / Line 52: @@
 * https://monarchinitiative.org
 * https://www.genome.gov/27544402/the-undiagnosed-diseases-program/
 [[Category: Journal Entry]]

@@ Line 31: / Line 31: @@
 *# I would direct a colleague unfamiliar with this site to view the database because I found it to be very easy to follow and a useful tool for performing a cross-species examination. I was originally unfamiliar with this site but was able to quickly and easily become acquainted with what it can do and what it has to offer.
 *# This could be either a professional or hobby database. The database can surely assist in professional usage but can also serve as a reference for someone who wants to perform a cross-species comparison on a certain gene, phenotype, or disease for recreational usage.
 ==Electronic Notebook==

@@ Line 13: / Line 13: @@
 # The content appears to completely cover its content domain.
 #*The database is composed of 5 records, overview, diseases, phenotypes, models, and genes, with each containing a field of information associated with their specific record. (https://monarchinitiative.org)
-#*The owners of the database provide a ven diagram in the corresponding paper illustrating the phenotypic coverage of all 19,008 human protein-coding genes. This diagram shows that 51%
+#*The owners of the database provide a ven diagram in the corresponding paper illustrating the phenotypic coverage of all 19,008 human protein-coding genes. This diagram shows that 51% of human protein-coding genes have at least 1 phenotype association in humans, 58% have orthologs with causal phenotypic associations reported in at least one non-human model, 40% have annotations both in human and non-human orthologs. This shows that 89% have phenotypic associations from humans and/or non-human orthologs and 11% have no annotations in any species. [https://watermark.silverchair.com/api/watermark?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAe8wggHrBgkqhkiG9w0BBwagggHcMIIB2AIBADCCAdEGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM4g9t7BQTLinLJl_ZAgEQgIIBoqMzOFbupWNrr909mhWDtlE7Kl5yvNILLa9LH2xmmZ9ORnU-U_hfwZGb1gXfFSJ_aSmpLD--fK1ZtoHsKisXxITurNiH3Rf0AvSLG9KvzsxwN8eVVtbXFzMagMKNXemlQyx9tSVF8jfmAt4S2Buc2HUh0Ac1M3X-ESY-pzWHtkHo-SCy2F4zWdzHMAdC_UyJGp_RIJjCw_KKXVkyn8GOuRz-3NZg7vy3kybiY4E8Hk6GIpKGN_sOtYlDfXvDRXaCJgrr0l8Gqx1M1eTmPNZCt5TtMtU7CR2DXGI83ZAEoqc70yFpxid-sYbkJ0TmSgEnF4sJ14BdFXZiPd5PFOS65O2aSiVOeZsC6BUo-MMUpMUkuYOBTczGnJk1J725gHy1EzrLqI9zSMnx0_pQfjDiNPAdnPiMPkvuRFhlzXU8KlSd2LNho-2bSoWjwpPd5uknWKpiHmpWOLmcSou5dfDB3O8jYTMkhLNC2YW6MLDODZ6n8bELunBABBOHgL3u3k-QjaHoWCgKkJLHqu1Y4-0-n-DUUTs2b_HV-UIlO5FSqbraw2g Monarch Initiative Corresponding Paper]
 # There are 7 species in the database: human, mouse, worm, fly, zebrafish, dog, and cow. (https://monarchinitiative.org/model)
 #The content of this database is useful in that it shows diseases described with phenotypes, gene variations associated with certain diseases, phenotype comparisons that suggest models, and models that suggest candidate genes. Each category of information has an interactive graph used to display the information in a concise and easily readable manner. (https://monarchinitiative.org/model)

@@ Line 13: / Line 13: @@
 # The content appears to completely cover its content domain.
 #*The database is composed of 5 records, overview, diseases, phenotypes, models, and genes, with each containing a field of information associated with their specific record. (https://monarchinitiative.org)
-#*The database owners provide an introduction statement saying that the Oregon Health & Science University (OHSU) provides the Monarch Tools under certain limitations. (https://monarchinitiative.org/page/disclaimer)
+#*The owners of the database provide a ven diagram in the corresponding paper illustrating the phenotypic coverage of all 19,008 human protein-coding genes. This diagram shows that 51%
-#**There is also a section for a disclaimer and then the limitations of liability. (https://monarchinitiative.org/page/disclaimer)
+ of human protein-coding genes have at least 1 phenotype association in humans, 58% have orthologs with causal phenotypic associations reported in at least one non-human model, 40% have annotations both in human and non-human orthologs. This shows that 89% have phenotypic associations from humans and/or non-human orthologs and 11% have no annotations in any species. [https://watermark.silverchair.com/api/watermark?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAe8wggHrBgkqhkiG9w0BBwagggHcMIIB2AIBADCCAdEGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM4g9t7BQTLinLJl_ZAgEQgIIBoqMzOFbupWNrr909mhWDtlE7Kl5yvNILLa9LH2xmmZ9ORnU-U_hfwZGb1gXfFSJ_aSmpLD--fK1ZtoHsKisXxITurNiH3Rf0AvSLG9KvzsxwN8eVVtbXFzMagMKNXemlQyx9tSVF8jfmAt4S2Buc2HUh0Ac1M3X-ESY-pzWHtkHo-SCy2F4zWdzHMAdC_UyJGp_RIJjCw_KKXVkyn8GOuRz-3NZg7vy3kybiY4E8Hk6GIpKGN_sOtYlDfXvDRXaCJgrr0l8Gqx1M1eTmPNZCt5TtMtU7CR2DXGI83ZAEoqc70yFpxid-sYbkJ0TmSgEnF4sJ14BdFXZiPd5PFOS65O2aSiVOeZsC6BUo-MMUpMUkuYOBTczGnJk1J725gHy1EzrLqI9zSMnx0_pQfjDiNPAdnPiMPkvuRFhlzXU8KlSd2LNho-2bSoWjwpPd5uknWKpiHmpWOLmcSou5dfDB3O8jYTMkhLNC2YW6MLDODZ6n8bELunBABBOHgL3u3k-QjaHoWCgKkJLHqu1Y4-0-n-DUUTs2b_HV-UIlO5FSqbraw2g Monarch Initiative Corresponding Paper]
 # There are 7 species in the database: human, mouse, worm, fly, zebrafish, dog, and cow. (https://monarchinitiative.org/model)
 #The content of this database is useful in that it shows diseases described with phenotypes, gene variations associated with certain diseases, phenotype comparisons that suggest models, and models that suggest candidate genes. Each category of information has an interactive graph used to display the information in a concise and easily readable manner. (https://monarchinitiative.org/model)

@@ Line 30: / Line 30: @@
 *# I believe a naive user could easily navigate this website. It is well organized, and you can quickly find and click on "About Monarch" under the "About" tab. The "About Monarch" page takes you through the background, the curation process of the data, and what you should expect to find upon doing a search. Other than that, the website is organized with clear headings, and it uses a design that is updated and colors that help direct and engage a user. If I search "Parkinson's", everything on the database relevant to Parkinson's will come up, and I can easily sort through the information and find the disease or phenotype that I am looking for. (https://monarchinitiative.org/page/about)
 *# There are no restrictions on access to this database. The bottom of their webpage states that it is licensed under a Creative Commons Attribution 3.0 License, except where forbidden by the original sources. (https://monarchinitiative.org/page/about)
-* '''Summary judgment'''
+* '''Summary judgement'''
 *# I would direct a colleague unfamiliar with this site to view the database because I found it to be very easy to follow and a useful tool for performing a cross-species examination. I was originally unfamiliar with this site but was able to quickly and easily become acquainted with what it can do and what it has to offer.
 *# This could be either a professional or hobby database. The database can surely assist in professional usage but can also serve as a reference for someone who wants to perform a cross-species comparison on a certain gene, phenotype, or disease for recreational usage.
 ==Acknowledgements==

@@ Line 4: / Line 4: @@
 * '''General information about the database'''
-*# Link to the database: https://monarchinitiative.org
+# Link to the database: https://monarchinitiative.org
-*# The database focuses on a cross-species examination of diseases, genes, and phenotypes.  (https://monarchinitiative.org/page/about)
+# The database focuses on a cross-species examination of diseases, genes, and phenotypes.  (https://monarchinitiative.org/page/about)
 #* The database uses model organisms for phenotype comparison within/across species. (https://monarchinitiative.org)
 #* The information on Monarch is considered a secondary source because it is curated from established “databases, spreadsheets, delimited text files, XML, JSON, and Web APIs”. This work is done personally by the staffed individuals at the database’s contributing institutions, which are listed in question number three. (https://monarchinitiative.org/page/about)
-*# The Monarch Initiative is maintained by several institutions, including Oregon Health & Science University, Lawrence Berkeley National Laboratory, The Jackson Laboratory, Charité - Universitätsmedizin Berlin, Queen Mary University of London, Garvan Institute, Renaissance Computing Institute - University of North Carolina at Chapel Hill, and University of Pittsburgh. More information about the contributing individuals at each institution can be found by clicking on the hyperlink. (https://monarchinitiative.org/page/team)
+# The Monarch Initiative is maintained by several institutions, including Oregon Health & Science University, Lawrence Berkeley National Laboratory, The Jackson Laboratory, Charité - Universitätsmedizin Berlin, Queen Mary University of London, Garvan Institute, Renaissance Computing Institute - University of North Carolina at Chapel Hill, and University of Pittsburgh. More information about the contributing individuals at each institution can be found by clicking on the hyperlink. (https://monarchinitiative.org/page/team)
-*# The institutions found funding for the database through a National Institutes of Health Office of the Director Grant, as well as through the National Institutes of Health Undiagnosed Diseases Program. (https://monarchinitiative.org/page/team) (https://www.genome.gov/27544402/the-undiagnosed-diseases-program/)
+# The institutions found funding for the database through a National Institutes of Health Office of the Director Grant, as well as through the National Institutes of Health Undiagnosed Diseases Program. (https://monarchinitiative.org/page/team) (https://www.genome.gov/27544402/the-undiagnosed-diseases-program/)
 * '''Scientific quality of the database'''
 # The content appears to completely cover its content domain.

@@ Line 5: / Line 5: @@
 * '''General information about the database'''
 *# Link to the database: https://monarchinitiative.org
-*# The database focuses on a cross species examination of diseases, genes, and phenotypes.  (https://monarchinitiative.org/page/about)
+*# The database focuses on a cross-species examination of diseases, genes, and phenotypes.  (https://monarchinitiative.org/page/about)
 *## The database uses model organisms for phenotype comparison within/across species. (https://monarchinitiative.org)
 *## The information on Monarch is considered a secondary source because it is curated from established “databases, spreadsheets, delimited text files, XML, JSON, and Web APIs”. This work is done personally by the staffed individuals at the database’s contributing institutions, which are listed in question number three. (https://monarchinitiative.org/page/about)