FDA-ARGOS FAQs - Revision history

Christie.woodside at 17:27, 19 September 2025

2025-09-19T17:27:42Z

← Older revision		Revision as of 17:27, 19 September 2025
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	===== What does the schema version in the datasets refer to? =====		===== What does the schema version in the datasets refer to? =====
	The schema relates to the organization of the ARGOS data within the data model. The version is reflective of the FDA-ARGOS data dictionary version that is currently applied to all updated datasets. As of September 2025, the current schema is v1.6.1 and can be found in the [https://github.com/FDA-ARGOS/data.argosdb/tree/main/data_dictionary/v1.6 FDA-ARGOS GitHub].		The schema relates to the organization of the ARGOS data within the data model. The version is reflective of the FDA-ARGOS data dictionary version that is currently applied to all updated datasets. As of September 2025, the current schema is v1.6.1 and can be found in the [https://github.com/FDA-ARGOS/data.argosdb/tree/main/data_dictionary/v1.6.1 FDA-ARGOS GitHub].

	===== Does Argos have a tutorial on how to use the site? =====		===== Does Argos have a tutorial on how to use the site? =====

Christie.woodside at 17:18, 19 September 2025

2025-09-19T17:18:58Z

← Older revision		Revision as of 17:18, 19 September 2025
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	===== What does the schema version in the datasets refer to? =====		===== What does the schema version in the datasets refer to? =====
	The schema relates to the organization of the ARGOS data within the data model. The version is reflective of the FDA-ARGOS data dictionary version that is currently applied to all updated datasets. As of September 2025, the current schema is v1.6.1 and can be found in the [https://github.com/FDA-ARGOS/data.argosdb/tree/main/data_dictionary/v1.6 FDA-~~ARGOs~~ GitHub].		The schema relates to the organization of the ARGOS data within the data model. The version is reflective of the FDA-ARGOS data dictionary version that is currently applied to all updated datasets. As of September 2025, the current schema is v1.6.1 and can be found in the [https://github.com/FDA-ARGOS/data.argosdb/tree/main/data_dictionary/v1.6 FDA-ARGOS GitHub].

	===== Does Argos have a tutorial on how to use the site? =====		===== Does Argos have a tutorial on how to use the site? =====

Christie.woodside at 17:18, 19 September 2025

2025-09-19T17:18:41Z

Christie.woodside at 16:13, 5 June 2025

2025-06-05T16:13:32Z

← Older revision		Revision as of 16:13, 5 June 2025
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			Back to [[FDA-ARGOS WIKI\|Home Page]] for FDA-ARGOS

	===== What is the ArgosDB and how is it organized? =====		===== What is the ArgosDB and how is it organized? =====

Christie.woodside at 19:11, 6 March 2025

2025-03-06T19:11:47Z

@@ Line 20: / Line 20: @@
 Keywords can be BCO ID, organism name, or even a term that describes biological processes. In the following example, three results appear upon the search for ebola.
-To further narrow down the result, select filters on the left side bar. Alternatively, users can search datasets by selecting relevant filters on the left side bar.[[File:Screenshot 2025-03-06 at 1.55.51 PM.png|left|thumb|719x719px|data.argosdb Home Page]]
+To further narrow down the result, select filters on the left side bar. Alternatively, users can search datasets by selecting relevant filters on the left side bar.[[File:Screenshot 2025-03-06 at 1.55.51 PM.png|thumb|719x719px|data.argosdb Home Page|none]][[File:Ebola search.png|thumb|722x722px|'ebola' searched in the search bar of the ARGOS database|none]]
 ====== How to select a dataset ======
 Next, to select a dataset, click on view details under DETAILS. Previous released versioned datasets are available upon clicking the dropdown button
-[[File:Dataset.png|left|thumb|722x722px|view of an example dataset after clicking on the '...view details' link on the homepage. The dropdown menu at the top lets you select data versions.]]
+[[File:Dataset.png|thumb|722x722px|view of an example dataset after clicking on the '...view details' link on the homepage. The dropdown menu at the top lets you select data versions.|none]]
 ====== How to view and download the BCO that is corresponding to its dataset ======
 To download the dataset, click on the DOWNLOADS tab and select the download format for the target dataset. BCO JSON will be downloaded and automatically opened as a .txt file upon clicking on Download BCO. Dataset will be downloaded and automatically opened either as .tsv or .csv file upon clicking on Download dataset file.
-[[File:Bco.png|left|thumb|720x720px|BCO JSON tab of the dataset.]]
+[[File:Bco.png|thumb|720x720px|BCO JSON tab of the dataset.|none]]
+[[File:Screenshot 2025-03-06 at 2.08.02 PM.png|thumb|724x724px|Downloads tab for the dataset. BCO and table can be downloaded here.|none]]

Christie.woodside at 19:09, 6 March 2025

2025-03-06T19:09:55Z

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	[[File:Ebola search.png\|left\|thumb\|722x722px\|'ebola' searched in the search bar of the ARGOS database]]		[[File:Ebola search.png\|left\|thumb\|722x722px\|'ebola' searched in the search bar of the ARGOS database]]




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	Next, to select a dataset, click on view details under DETAILS. Previous released versioned datasets are available upon clicking the dropdown button		Next, to select a dataset, click on view details under DETAILS. Previous released versioned datasets are available upon clicking the dropdown button
	[[File:Dataset.png\|left\|thumb\|722x722px\|view of an example dataset after clicking on the '...view details' link on the homepage. The dropdown menu at the top lets you select data versions.]]		[[File:Dataset.png\|left\|thumb\|722x722px\|view of an example dataset after clicking on the '...view details' link on the homepage. The dropdown menu at the top lets you select data versions.]]

Christie.woodside at 19:09, 6 March 2025

2025-03-06T19:09:38Z

← Older revision		Revision as of 19:09, 6 March 2025
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	[[File:Ebola search.png\|left\|thumb\|722x722px\|'ebola' searched in the search bar of the ARGOS database]]		[[File:Ebola search.png\|left\|thumb\|722x722px\|'ebola' searched in the search bar of the ARGOS database]]







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	Next, to select a dataset, click on view details under DETAILS. Previous released versioned datasets are available upon clicking the dropdown button		Next, to select a dataset, click on view details under DETAILS. Previous released versioned datasets are available upon clicking the dropdown button
	[[File:Dataset.png\|left\|thumb\|722x722px\|view of an example dataset after clicking on the '...view details' link on the homepage. The dropdown menu at the top lets you select data versions.]]		[[File:Dataset.png\|left\|thumb\|722x722px\|view of an example dataset after clicking on the '...view details' link on the homepage. The dropdown menu at the top lets you select data versions.]]

Christie.woodside at 19:09, 6 March 2025

2025-03-06T19:09:06Z

@@ Line 14: / Line 14: @@
 ===== Does Argos have a tutorial on how to use the site? =====
 Yes! Please follow the below basic instructions of how to navigate the DB:
 ====== How to find and search a dataset ======
 On data.argosdb.org home page, you can search a dataset by entering the keyword in Search Datasets.
 Keywords can be BCO ID, organism name, or even a term that describes biological processes. In the following example, three results appear upon the search for ebola.
-[[File:Screenshot 2025-03-06 at 1.55.51 PM.png|left|thumb|719x719px|data.argosdb Home Page]]
+To further narrow down the result, select filters on the left side bar. Alternatively, users can search datasets by selecting relevant filters on the left side bar.[[File:Screenshot 2025-03-06 at 1.55.51 PM.png|left|thumb|719x719px|data.argosdb Home Page]]
@@ Line 37: / Line 52: @@
 ====== How to select a dataset ======
 Next, to select a dataset, click on view details under DETAILS. Previous released versioned datasets are available upon clicking the dropdown button
 ====== How to view and download the BCO that is corresponding to its dataset ======
 To download the dataset, click on the DOWNLOADS tab and select the download format for the target dataset. BCO JSON will be downloaded and automatically opened as a .txt file upon clicking on Download BCO. Dataset will be downloaded and automatically opened either as .tsv or .csv file upon clicking on Download dataset file.

Christie.woodside at 18:58, 6 March 2025

2025-03-06T18:58:37Z

@@ Line 3: / Line 3: @@
 ArgosDB was developed as a result of expanded funding for the FDA-ARGOS project, which is described in detail in the [[About Argos DataBase|About]] page of this website. The database stores cross-kingdom QC attributes of clinically relevant organisms organized into respective datasets. The current datasets (as of March 2025) are: ngsQC_ARGOS, ngsQC_ARGOS_unreviewed, assemblyQC_ARGOS, assemblyQC_ARGOS_unreviewed, biosampleMeta_ARGOS, and biosampleMeta_ARGOS unreviewed. The original four key datasets are ngsQC_HIVE, assemblyQC_HIVE, siteQC_HIVE, and biosampleMeta_HIVE. These datasets are associated with core QC protocols, which are documented via Biocompute Objects (BCO) and organized under their BCO IDs.
-When new QC data has been produced per an organism of interest, the respective dataset(s) is/are appended, which is documented per data release in the FDA-ARGOS GitHub (<nowiki>https://github.com/FDA-ARGOS</nowiki>). All datasets are in alignment with the current data dictionary, which guides the QC process for that dataset as well as the column headers for a given dataset. Datasets are available as either .tsv, or FASTA files if associated with a genome assembly, and all datasets and BCOs are available for download. All data provenance and curation is captured and reproducible via their BCO. Additional datasets include data from the original FDA BioProject, the Data Dictionary, Drug Resistance Mutations, Genome Assemblies (multiple), and a mapping key which assists in linking all the available data via important accessions. A total of 15 datasets are available as of 10/2023.
+When new QC data has been produced per an organism of interest, the respective dataset(s) is/are appended, which is documented per data release in the FDA-ARGOS GitHub (<nowiki>https://github.com/FDA-ARGOS</nowiki>). All datasets are in alignment with the current data dictionary (v1.6 as of March 2025), which guides the QC process for that dataset as well as the column headers for a given dataset. Datasets are available as either .tsv or FASTA files if associated with a genome assembly, and all datasets and BCOs are available for download. All data provenance and curation are captured and reproducible via their BCO. Additional datasets include data from the original FDA BioProject, the Data Dictionary, Drug Resistance Mutations, Genome Assemblies (multiple), and a mapping key that assists in linking all the available data via important accessions.
 ===== How can I view or access the previous versions of the data? =====
@@ Line 9: / Line 11: @@
 ===== What does the schema version in the datasets refer to? =====
-The schema relates to the organization of the ARGOS data within the data model. The version is reflective of the FDA-ARGOS data dictionary version that is currently applied to all updated datasets.
+The schema relates to the organization of the ARGOS data within the data model. The version is reflective of the FDA-ARGOS data dictionary version that is currently applied to all updated datasets. As of March 2025, the current schema is v1.6 and can be found in the [https://github.com/FDA-ARGOS/data.argosdb/tree/main/data_dictionary/v1.6 FDA-ARGOs GitHub].
 ===== Does Argos have a tutorial on how to use the site? =====
-Yes! Please follow the below basic instructions of how to navigate the DB: How to find and search a dataset On data.argosdb.org home page, you can search a dataset by entering the keyword in Search Datasets. Keywords can be BCO ID, organism name, or even a term that describes biological processes. In the following example, three results appear upon the search for ebola. To further narrow down the result, select filters on the left side bar. Alternatively, users can search datasets by selecting relevant filters on the left side bar. How to select a dataset Next, to select a dataset, click on view details under DETAILS. Previous released versioned datasets are available upon clicking the dropdown button How to view and download the BCO that is corresponding to its dataset To download the dataset, click on the DOWNLOADS tab and select the download format for the target dataset. BCO JSON will be downloaded and automatically opened as a .txt file upon clicking on Download BCO. Dataset will be downloaded and automatically opened either as .tsv or .csv file upon clicking on Download dataset file.
+Yes! Please follow the below basic instructions of how to navigate the DB:

Christie.woodside at 17:25, 6 March 2025

2025-03-06T17:25:31Z

← Older revision		Revision as of 17:25, 6 March 2025
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	===== What is the ArgosDB and how is it organized? =====		===== What is the ArgosDB and how is it organized? =====
	ArgosDB was developed as a result of expanded funding for the FDA-ARGOS project, which is described in detail in the About ~~tab~~ of this website. The database stores cross-kingdom QC attributes of clinically relevant organisms organized ~~in 4~~ key datasets: ngsQC_HIVE, assemblyQC_HIVE, siteQC_HIVE, and biosampleMeta_HIVE. These datasets are associated with 4 core QC protocols which are documented via Biocompute Objects (BCO) and organized under their BCO IDs. When new QC data has been produced per an organism of interest, the respective dataset(s) is/are appended, which is documented per data release in the FDA-ARGOS GitHub (<nowiki>https://github.com/FDA-ARGOS</nowiki>). All datasets are in alignment with the current data dictionary, which guides the QC process for that dataset as well as the column headers for a given dataset. Datasets are available as either .tsv, or FASTA files if associated with a genome assembly, and all datasets and BCOs are available for download. All data provenance and curation is captured and reproducible via their BCO. Additional datasets include data from the original FDA BioProject, the Data Dictionary, Drug Resistance Mutations, Genome Assemblies (multiple), and a mapping key which assists in linking all the available data via important accessions. A total of 15 datasets are available as of 10/2023.		ArgosDB was developed as a result of expanded funding for the FDA-ARGOS project, which is described in detail in the [[About Argos DataBase\|About]] page of this website. The database stores cross-kingdom QC attributes of clinically relevant organisms organized into respective datasets. The current datasets (as of March 2025) are: ngsQC_ARGOS, ngsQC_ARGOS_unreviewed, assemblyQC_ARGOS, assemblyQC_ARGOS_unreviewed, biosampleMeta_ARGOS, and biosampleMeta_ARGOS unreviewed. The original four key datasets are ngsQC_HIVE, assemblyQC_HIVE, siteQC_HIVE, and biosampleMeta_HIVE. These datasets are associated with core QC protocols, which are documented via Biocompute Objects (BCO) and organized under their BCO IDs.

			When new QC data has been produced per an organism of interest, the respective dataset(s) is/are appended, which is documented per data release in the FDA-ARGOS GitHub (<nowiki>https://github.com/FDA-ARGOS</nowiki>). All datasets are in alignment with the current data dictionary, which guides the QC process for that dataset as well as the column headers for a given dataset. Datasets are available as either .tsv, or FASTA files if associated with a genome assembly, and all datasets and BCOs are available for download. All data provenance and curation is captured and reproducible via their BCO. Additional datasets include data from the original FDA BioProject, the Data Dictionary, Drug Resistance Mutations, Genome Assemblies (multiple), and a mapping key which assists in linking all the available data via important accessions. A total of 15 datasets are available as of 10/2023.

	===== How can I view or access the previous versions of the data? =====		===== How can I view or access the previous versions of the data? =====

← Older revision		Revision as of 17:18, 19 September 2025
Line 3:		Line 3:

	===== What is the ArgosDB and how is it organized? =====		===== What is the ArgosDB and how is it organized? =====
	ArgosDB was developed as a result of expanded funding for the FDA-ARGOS project, which is described in detail in the [[About Argos DataBase\|About]] page of this website. The database stores cross-kingdom QC attributes of clinically relevant organisms organized into respective datasets. The current datasets (as of ~~March~~ 2025) are: ngsQC_ARGOS, ~~ngsQC_ARGOS_unreviewed~~, assemblyQC_ARGOS, ~~assemblyQC_ARGOS_unreviewed~~, biosampleMeta_ARGOS, and ~~biosampleMeta_ARGOS unreviewed. The original four key datasets are ngsQC_HIVE, assemblyQC_HIVE, siteQC_HIVE, and biosampleMeta_HIVE~~. These datasets are associated with core QC protocols, which are documented via Biocompute Objects (BCO) and organized under their BCO IDs.		ArgosDB was developed as a result of expanded funding for the FDA-ARGOS project, which is described in detail in the [[About Argos DataBase\|About]] page of this website. The database stores cross-kingdom QC attributes of clinically relevant organisms organized into respective datasets. The current datasets (as of September 2025) are: ngsQC_ARGOS, ngsQC_ARGOS_extended, assemblyQC_ARGOS, assemblyQC_ARGOS_extended, biosampleMeta_ARGOS, and biosampleMeta_ARGOS_extended. These datasets are associated with core QC protocols, which are documented via Biocompute Objects (BCO) and organized under their BCO IDs.

	When new QC data has been produced ~~per~~ an organism of interest, the respective dataset(s) is/are appended, which is documented per data release in the FDA-ARGOS GitHub (<nowiki>https://github.com/FDA-ARGOS</nowiki>). All datasets are in alignment with the current data dictionary (v1.6 as of ~~March~~ 2025), which guides the QC process for that dataset as well as the column headers for a given dataset. Datasets are available as either .tsv or FASTA files if associated with a genome assembly, and all datasets and BCOs are available for download. All data provenance and curation are captured and reproducible via their BCO. Additional datasets include data from the original FDA BioProject, the Data Dictionary, Drug Resistance Mutations, Genome Assemblies (multiple), and a mapping key that assists in linking all the available data via important accessions.		When new QC data has been produced for an organism of interest, the respective dataset(s) is/are appended, which is documented per data release in the FDA-ARGOS GitHub (<nowiki>https://github.com/FDA-ARGOS</nowiki>) and on the database itself. All datasets are in alignment with the current data dictionary (v1.6.1 as of September 2025), which guides the QC process for that dataset as well as the column headers for a given dataset. Datasets are available as either .tsv or FASTA files if associated with a genome assembly, and all datasets and BCOs are available for download. All data provenance and curation are captured and reproducible via their BCO. Additional datasets include data from the original FDA BioProject, the Data Dictionary, Drug Resistance Mutations, Genome Assemblies (multiple), and a mapping key that assists in linking all the available data via important accessions.

	A total of 24 datasets are available as of 03/2025.		A total of 14 datasets are available as of 09/2025.

	===== How can I view or access the previous versions of the data? =====		===== How can I view or access the previous versions of the data? =====
	First, go to the Release History tab on the ARGOS home page. Next, click details on the desired data object. Then select the desired version and data from the version transition dropbox on the top left corner and view metrics such as field count, fields added, fields removed, row count, row count prev, rows count change, ID count, IDs added, and IDs removed.		First, go to the Release History tab on the ARGOS home page. Next, click 'details' on the desired data object. Then select the desired version and data from the version transition dropbox on the top left corner and view metrics such as field count, fields added, fields removed, row count, row count prev, rows count change, ID count, IDs added, and IDs removed.

	===== What does the schema version in the datasets refer to? =====		===== What does the schema version in the datasets refer to? =====
	The schema relates to the organization of the ARGOS data within the data model. The version is reflective of the FDA-ARGOS data dictionary version that is currently applied to all updated datasets. As of ~~March~~ 2025, the current schema is v1.6 and can be found in the [https://github.com/FDA-ARGOS/data.argosdb/tree/main/data_dictionary/v1.6 FDA-ARGOs GitHub].		The schema relates to the organization of the ARGOS data within the data model. The version is reflective of the FDA-ARGOS data dictionary version that is currently applied to all updated datasets. As of September 2025, the current schema is v1.6.1 and can be found in the [https://github.com/FDA-ARGOS/data.argosdb/tree/main/data_dictionary/v1.6 FDA-ARGOs GitHub].

	===== Does Argos have a tutorial on how to use the site? =====		===== Does Argos have a tutorial on how to use the site? =====
	Yes! Please follow the below ~~basic instructions~~ of how to navigate the DB:		Yes! Please follow the instructions below of how to navigate the DB.

	====== How to find and search a dataset ======		====== How to find and search a dataset ======
	On data.argosdb.org home page, you can search a dataset by entering the keyword in Search Datasets.		On data.argosdb.org home page, you can search for a dataset by entering the keyword in Search Datasets.

	Keywords can be BCO ID, organism name, or even a term that describes biological processes. In the following example, three results appear upon the search for ~~ebola~~.		Keywords can be BCO ID, organism name, or even a term that describes biological processes. In the following example, three results appear upon the search for Ebola.
	To further narrow down the result, select filters on the left ~~side bar~~. Alternatively, users can search datasets by selecting relevant filters on the left ~~side bar~~.[[File:Screenshot 2025-03-06 at 1.55.51 PM.png\|thumb\|719x719px\|data.argosdb Home Page~~\|none~~]][[File:~~Ebola search~~.png\|thumb\|722x722px\|'~~ebola~~' searched in the search bar of the ARGOS database~~\|none~~]]		To further narrow down the result, select filters on the left sidebar. Alternatively, users can search datasets by selecting relevant filters on the left sidebar.
			[[File:Screenshot 2025-09-19 at 1.16.41 PM.png\|none\|thumb\|719x719px\|data.argosdb Home Page]]
			[[File:Screenshot 2025-09-19 at 1.17.57 PM.png\|none\|thumb\|722x722px\|'Ebola' searched in the search bar of the ARGOS database]]

	====== How to select a dataset ======		====== How to select a dataset ======