Examples of implementing a unique study ID - Revision history

Leonardo.restivo at 07:51, 29 April 2021

2021-04-29T07:51:49Z

Bjoerngerlach: /* From INBC of University of Heidelberg */

2021-04-28T12:51:26Z

‎From INBC of University of Heidelberg

Bjoerngerlach: /* From Behavioral and Physiological Phenotyping Unit of Weizmann Institute of Science */

2021-04-28T12:48:30Z

‎From Behavioral and Physiological Phenotyping Unit of Weizmann Institute of Science

Bjoerngerlach: /* From Neuro-Behavioral-Analysis Unit of University of Lausanne */

2021-04-28T12:44:27Z

‎From Neuro-Behavioral-Analysis Unit of University of Lausanne

Bjoerngerlach: /* From Behavioral and Physiological Phenotyping Unit of Weizmann Institute of Science */

2021-04-28T12:42:41Z

‎From Behavioral and Physiological Phenotyping Unit of Weizmann Institute of Science

Bjoerngerlach: /* From Behavioral and Physiological Phenotyping Unit of Weizmann Institute of Science */

2021-04-28T12:42:06Z

‎From Behavioral and Physiological Phenotyping Unit of Weizmann Institute of Science

Bjoerngerlach: /* From Behavioral and Physiological Phenotyping Unit of Weizmann Institute of Science */

2021-04-28T12:36:30Z

‎From Behavioral and Physiological Phenotyping Unit of Weizmann Institute of Science

Bjoerngerlach: /* From Behavioral and Physiological Phenotyping Unit of Weizmann Institute of Science */

2021-04-28T12:31:55Z

‎From Behavioral and Physiological Phenotyping Unit of Weizmann Institute of Science

Bjoerngerlach: /* From Neuro-Behavioral-Analysis Unit of University of Lausanne */

2021-04-28T12:24:17Z

‎From Neuro-Behavioral-Analysis Unit of University of Lausanne

Bjoerngerlach: /* From Neuro-Behavioral-Analysis Unit of University of Lausanne */

2021-04-28T12:23:47Z

‎From Neuro-Behavioral-Analysis Unit of University of Lausanne

@@ Line 6: / Line 6: @@
 ::: e.g. '''201108-cpitzer-catwalk with mice zQ98'''
-==From Neuro-Behavioral-Analysis Unit of University of Lausanne==
+==From Neuro-Behavioral-Analysis Unit, Department of Fundamental Neuroscience, University of Lausanne==
 [https://orcid.org/0000-0002-3709-5504 Leonardo Restivo], the core facility head of the [http://neurobau.com Neuro-BAU], uses this nomenclature to store metadata at his core facility.[[File:LRestivo_StudyID_210428.jpg|frame|]]
-This system is only used to store metadata allowing me to have an overview of all experiments done in my facility (project id, project info, experimental protocols) but is not used for raw data
+This system is only used to store metadata(project id, project info, experimental protocols) but it is not used for raw data.
-As concerns the experimental record ID (generated by myself):
+The experimental record ID is generated as follows:
-initials of the PI + acronym of the department + Institution acronym + sequential integer
+Initials of the PI + Acronym of the department + Institution acronym + Sequential integer
 Example:
-Leonardo Restivo, Department of Fundamental Neuroscience (swap letters in french acronym...), University of Lausanne, project one
+Leonardo Restivo, Department of Fundamental Neuroscience (swap letters in french acronym), University of Lausanne, project one
 ::: e.g. '''LR_DNF_UNIL_1'''
-This id is part of a simple two-table database (it has its unique own row_id see attached image):
+This id is part of a simple two-table database (it has its unique own row_id see image):
-one of the fields is `code-name` that reports a friendly name (e.g. "gut microbiota and spatial orientation") of the project that is used to communicate with the lab working on the project
+The `code-name` field contains a friendly name (e.g. "gut microbiota and spatial orientation") for the project. This name is used to communicate with the lab working on the project.
-Then, each experiment belonging to this project inherits the project id, but have their unique id (which is a unique auto-incrementing integer) + friendly name (e.g. "water maze")
+Each experiment belonging to this project inherits the project id. Every experiment has its own unique id (which is a unique auto-incrementing integer) + friendly name (e.g. "water maze")
 The `experiment` table has a field named `data`. This is a link to a text-markdown file that logs the experimental protocol and any change to it.

@@ Line 1: / Line 1: @@
 ==From INBC of University of Heidelberg==
-Claudia Pitzer, the core facility head, uses this explanation in a document handed out to the user:
+[https://orcid.org/0000-0002-7663-1031 Claudia Pitzer], the core facility head of the [http://www.medizinische-fakultaet-hd.uni-heidelberg.de/Home.111344.0.html Interdisciplinary Neurobehavioral Core], uses this explanation in a document handed out to the user:
 File naming: in order that each data is unique and retrievable we suggest that you adhere to the following file naming convention: [date YYMMDD]-[the first letter of your first name together with your last name]-[free text]. If your surname is long you may use only the first 6 letters of it.

@@ Line 25: / Line 25: @@
 ==From Behavioral and Physiological Phenotyping Unit of Weizmann Institute of Science==
-Michael Tsoory, the core facility head, describes the procudure for users as follows:
+[https://orcid.org/0000-0003-0441-8757 Michael Tsoory], the core facility head at [http://www.weizmann.ac.il/vet/advanced-services/behavior-and-physiology/about Weizman Institute], describes the procudure for users as follows:
 ''“The PI must communicate the IACUC Approval number to the CF and to the person(s) undertaking the Studies and Experiments. This number must be incorporated into the unique study-experiment ID by whomever assumes responsibility on maintaining the Experimental Records”.''

@@ Line 7: / Line 7: @@
 ==From Neuro-Behavioral-Analysis Unit of University of Lausanne==
-Leonardo Restivo, the core facility head, uses this nomenclature to store metadata at his core facility.[[File:LRestivo_StudyID_210428.jpg|frame|]]
+[https://orcid.org/0000-0002-3709-5504 Leonardo Restivo], the core facility head of the [http://neurobau.com Neuro-BAU], uses this nomenclature to store metadata at his core facility.[[File:LRestivo_StudyID_210428.jpg|frame|]]
 This system is only used to store metadata allowing me to have an overview of all experiments done in my facility (project id, project info, experimental protocols) but is not used for raw data

@@ Line 41: / Line 41: @@
 (we may want to include additional folders for “conclusions”, “publications”)
-IA12340221-1
+'''IA12340221-1'''
 :'''PLANS'''
 ::SP1

@@ Line 33: / Line 33: @@
 Therefore a record keeping system may apply the below noted suggestion:
-For example '''IACUC Approval 12340221-1 (IA)'' includes 3 studies (3 Study Protocols: SP1, SP2, SP3), one of which (SP2) is assessing the relevance of gene X to learning and memory. So SP2 includes assessing wt and KO mice in the 1) Y-maze; 2) NOR; 3) MWM; as well as some anxiety tests 4) Acoustic Startle Response; 5) Dark-Light Transfer test; and basic motor assessments 6) home-cage locomotion; 7) Open-Filed. All together 7 Experimental Procedures (EP).
+For example, '''IACUC Approval 12340221-1 (IA)'' includes 3 studies (3 Study Protocols: SP1, SP2, SP3), one of which ('''SP2''') is assessing the relevance of gene X to learning and memory. So SP2 includes assessing wt and KO mice in the 1) Y-maze; 2) NOR; 3) MWM; as well as some anxiety tests 4) Acoustic Startle Response; 5) Dark-Light Transfer test; and basic motor assessments 6) home-cage locomotion; 7) Open-Filed. All together 7 '''Experimental Procedures (EP)'''.
-The Experimental Records will be filed in a FOLDER named: IA12340221-1
+The Experimental Records will be filed in a '''FOLDER named: IA12340221-1'''
-* <pre style="color: green"> PLANS</pre>, experimental designs, planed experimental procedures, and everything else that has to do with planning etc. (like calculations of Ns), will filed in folders named SP with subfolders for every experiment EP.,
+*  '''PLANS''', experimental designs, planed experimental procedures, and everything else that has to do with planning etc. (like calculations of Ns), will filed in folders named SP with subfolders for every experiment EP.,
-* All data generated in these studies will be filed a <pre style="color: red"> RAW DATA</pre> folder; a DATA folder will have subfolders of SP and subsequent EP.
+* All data generated in these studies will be filed a '''RAW DATA''' folder; a DATA folder will have subfolders of SP and subsequent EP.
-* All analyses of data generated in these studies will be filed an <pre style="color: blue"> ANALYSES</pre> folder
+* All analyses of data generated in these studies will be filed an '''ANALYSES''' folder
 (we may want to include additional folders for “conclusions”, “publications”)
 IA12340221-1
-<pre style="color: green">:PLANS
+:'''PLANS'''
 ::SP1
 ::SP2
@@ Line 48: / Line 48: @@
 :::EP2
 :::…
-:::EP7 </pre>
+:::EP7
-<pre style="color: red">:RAW DATA
+:'''RAW DATA'''
 ::SP1
 ::SP2
@@ Line 55: / Line 55: @@
 :::EP2
 :::…
-:::EP7</pre>
+:::EP7
-<pre style="color: blue">:ANALYSES
+:'''ANALYSES
 ::SP1
 ::SP2
@@ Line 62: / Line 62: @@
 :::EP2
 :::…
-:::EP7</pre>
+:::EP7
 The data generated in this MWM experiment will be
 e.g. IA12340221-1/DATA/SP2/EP3
 The files in that folder can take a name comprised of the DATE and initials of the person performing the test “John Doe”: JD_YYMMDD.
 Moreover, in the data sheet I STRONGLY recommend that the IACUC#, SP# and EP# would appear in the columns next to the mouse#, DOB, SEX and Genotype columns (in the Noldus Ethovision these columns may be added already in the “trial list” stage and would be automated included in all output/export files):
 {|class="wikitable"
 !colspan="7"|Identifiers