Terms of use metadata

Some new metadata columns have been added to help identify which sample sets have usage restrictions (e.g., publication embargo) and which are available for unrestricted use. The metadata columns are:

• terms_of_use_expiry_date - Gives the date on which any terms of use will expire. After this date, there will be no usage restrictions on data relating to the sample set.
• terms_of_use_url - Gives the address of a web page that describes any usage restrictions which apply to the sample set.

If the value of either of these fields is empty then there are no terms of use applying to the sample set.

These new metadata columns can be accessed via the malariagen_data Python API. The API also addes an additional computed field:

• unrestricted_use - This is a computed column which is added for convenience. The value is True if the terms of use have expired, or if there were never any usage restrictions applied.

The metadata columns are available in the dataframes returned by the sample_sets() and sample_metadata() functions. Below are some examples for data from the Anopheles gambiae complex accessed via the Ag3 API. Similar code can be used for Anopheles funestus samples via the Af1 API.

import malariagen_data
ag3 = malariagen_data.Ag3()

Sample set metadata:

df_sample_sets = ag3.sample_sets()
df_sample_sets[["sample_set", "terms_of_use_expiry_date", "unrestricted_use"]]

	sample_set	terms_of_use_expiry_date	unrestricted_use
0	AG1000G-AO	2025-01-01	False
1	AG1000G-BF-A	2025-01-01	False
2	AG1000G-BF-B	2025-01-01	False
3	AG1000G-BF-C	2025-01-01	False
4	AG1000G-CD	2025-01-01	False
...	...	...	...
78	1323-VO-GM-NGWA-VMF00235	2026-04-09	False
79	1323-VO-GM-NGWA-VMF00242	2026-04-09	False
80	1329-VO-GA-CHRISTOPHE-VMF00228	2026-04-09	False
81	bergey-2019	NaN	True
82	campos-2021	NaN	True

83 rows × 3 columns

Query to find sample sets with no usage restrictions:

df_sample_sets.query("unrestricted_use")

	sample_set	sample_count	study_id	study_url	terms_of_use_expiry_date	terms_of_use_url	release	unrestricted_use
32	fontaine-2015-rebuild	72	fontaine-2015-rebuild	https://doi.org/10.1126/science.1258524	NaN	https://www.science.org/doi/10.1126/science.12...	3.10	True
34	1237-VO-BJ-DJOGBENOU-VMF00050	90	1237-VO-BJ-DJOGBENOU	https://www.malariagen.net/partner_study/1237-...	2024-07-22	https://malariagen.github.io/vector-data/ag3/a...	3.2	True
35	1237-VO-BJ-DJOGBENOU-VMF00067	142	1237-VO-BJ-DJOGBENOU	https://www.malariagen.net/partner_study/1237-...	2024-07-22	https://malariagen.github.io/vector-data/ag3/a...	3.2	True
36	1244-VO-GH-YAWSON-VMF00051	666	1244-VO-GH-YAWSON	https://www.malariagen.net/partner_study/1244-...	2024-07-22	https://malariagen.github.io/vector-data/ag3/a...	3.2	True
37	1245-VO-CI-CONSTANT-VMF00054	38	1245-VO-CI-CONSTANT	https://www.malariagen.net/partner_study/1245-...	2024-07-22	https://malariagen.github.io/vector-data/ag3/a...	3.2	True
38	1253-VO-TG-DJOGBENOU-VMF00052	179	1253-VO-TG-DJOGBENOU	https://www.malariagen.net/partner_study/1253-...	2024-07-22	https://malariagen.github.io/vector-data/ag3/a...	3.2	True
39	1178-VO-UG-LAWNICZAK-VMF00025	57	1178-VO-UG-LAWNICZAK	https://www.malariagen.net/partner_study/1178-...	2023-10-26	https://malariagen.github.io/vector-data/ag3/a...	3.3	True
65	barron-2019	4	barron-2019	https://doi.org/10.1038/s41598-019-49065-5	NaN	https://www.nature.com/articles/s41598-019-490...	3.7	True
66	crawford-2016	25	crawford-2016	https://doi.org/10.1111/mec.13572	NaN	https://onlinelibrary.wiley.com/doi/10.1111/me...	3.7	True
72	tennessen-2021	208	tennessen-2021	https://doi.org/10.1111/mec.15756	NaN	https://onlinelibrary.wiley.com/doi/10.1111/me...	3.8	True
81	bergey-2019	113	bergey-2019	https://doi.org/10.1111/eva.12878	NaN	https://onlinelibrary.wiley.com/doi/10.1111/ev...	3.9	True
82	campos-2021	163	campos-2021	https://doi.org/10.1038/s42003-021-02168-0, ht...	NaN	https://www.nature.com/articles/s42003-021-021...	3.9	True

Sample metadata:

df_samples = ag3.sample_metadata()
df_samples[["sample_id", "sample_set", "terms_of_use_expiry_date", "terms_of_use_url", "unrestricted_use"]]

	sample_id	sample_set	terms_of_use_expiry_date	terms_of_use_url	unrestricted_use
0	VBS00256-4651STDY7017184	1177-VO-ML-LEHMANN-VMF00004	2025-11-17	https://malariagen.github.io/vector-data/ag3/a...	False
1	VBS00257-4651STDY7017185	1177-VO-ML-LEHMANN-VMF00004	2025-11-17	https://malariagen.github.io/vector-data/ag3/a...	False
2	VBS00259-4651STDY7017186	1177-VO-ML-LEHMANN-VMF00004	2025-11-17	https://malariagen.github.io/vector-data/ag3/a...	False
3	VBS00262-4651STDY7017187	1177-VO-ML-LEHMANN-VMF00004	2025-11-17	https://malariagen.github.io/vector-data/ag3/a...	False
4	VBS00277-4651STDY7017189	1177-VO-ML-LEHMANN-VMF00004	2025-11-17	https://malariagen.github.io/vector-data/ag3/a...	False
...	...	...	...	...	...
19766	SAMN15222632	tennessen-2021	NaN	https://onlinelibrary.wiley.com/doi/10.1111/me...	True
19767	SAMN15222633	tennessen-2021	NaN	https://onlinelibrary.wiley.com/doi/10.1111/me...	True
19768	SAMN15222634	tennessen-2021	NaN	https://onlinelibrary.wiley.com/doi/10.1111/me...	True
19769	SAMN15222635	tennessen-2021	NaN	https://onlinelibrary.wiley.com/doi/10.1111/me...	True
19770	SAMN15222636	tennessen-2021	NaN	https://onlinelibrary.wiley.com/doi/10.1111/me...	True

19771 rows × 5 columns

Query to find samples with no usage restrictions:

df_samples.query("unrestricted_use")

	sample_id	partner_sample_id	contributor	country	location	year	month	latitude	longitude	sex_call	...	admin1_name	admin1_iso	admin2_name	taxon	cohort_admin1_year	cohort_admin1_month	cohort_admin1_quarter	cohort_admin2_year	cohort_admin2_month	cohort_admin2_quarter
670	VBS10116-4954STDY7089644	UG4A2016A1_96	Mara Lawniczak	Uganda	Busia	2013	1	0.466	34.089	F	...	Eastern Region	UG-E	Busia	gambiae	UG-E_gamb_2013	UG-E_gamb_2013_01	UG-E_gamb_2013_Q1	UG-E_Busia_gamb_2013	UG-E_Busia_gamb_2013_01	UG-E_Busia_gamb_2013_Q1
671	VBS10117-4954STDY7089645	UG4A2016B1_95	Mara Lawniczak	Uganda	Busia	2016	6	0.466	34.089	F	...	Eastern Region	UG-E	Busia	gambiae	UG-E_gamb_2016	UG-E_gamb_2016_06	UG-E_gamb_2016_Q2	UG-E_Busia_gamb_2016	UG-E_Busia_gamb_2016_06	UG-E_Busia_gamb_2016_Q2
672	VBS10118-4954STDY7089646	UG4A2016C1_94	Mara Lawniczak	Uganda	Busia	2016	6	0.466	34.089	F	...	Eastern Region	UG-E	Busia	gambiae	UG-E_gamb_2016	UG-E_gamb_2016_06	UG-E_gamb_2016_Q2	UG-E_Busia_gamb_2016	UG-E_Busia_gamb_2016_06	UG-E_Busia_gamb_2016_Q2
673	VBS10119-4954STDY7089647	UG4A2016D1_93	Mara Lawniczak	Uganda	Busia	2016	6	0.466	34.089	F	...	Eastern Region	UG-E	Busia	gambiae	UG-E_gamb_2016	UG-E_gamb_2016_06	UG-E_gamb_2016_Q2	UG-E_Busia_gamb_2016	UG-E_Busia_gamb_2016_06	UG-E_Busia_gamb_2016_Q2
674	VBS10120-4954STDY7089648	UG4A2016E1_92	Mara Lawniczak	Uganda	Busia	2016	6	0.466	34.089	F	...	Eastern Region	UG-E	Busia	gambiae	UG-E_gamb_2016	UG-E_gamb_2016_06	UG-E_gamb_2016_Q2	UG-E_Busia_gamb_2016	UG-E_Busia_gamb_2016_06	UG-E_Busia_gamb_2016_Q2
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
19766	SAMN15222632	D342	Jacob Tennessen	Burkina Faso	Tengrela	2016	-1	10.700	-4.800	F	...	Cascades	BF-02	Comoe	coluzzii	BF-02_colu_2016	BF-02_colu_2016	BF-02_colu_2016	BF-02_Comoe_colu_2016	BF-02_Comoe_colu_2016	BF-02_Comoe_colu_2016
19767	SAMN15222633	D343	Jacob Tennessen	Burkina Faso	Tengrela	2016	-1	10.700	-4.800	F	...	Cascades	BF-02	Comoe	coluzzii	BF-02_colu_2016	BF-02_colu_2016	BF-02_colu_2016	BF-02_Comoe_colu_2016	BF-02_Comoe_colu_2016	BF-02_Comoe_colu_2016
19768	SAMN15222634	D346	Jacob Tennessen	Burkina Faso	Tengrela	2016	-1	10.700	-4.800	F	...	Cascades	BF-02	Comoe	coluzzii	BF-02_colu_2016	BF-02_colu_2016	BF-02_colu_2016	BF-02_Comoe_colu_2016	BF-02_Comoe_colu_2016	BF-02_Comoe_colu_2016
19769	SAMN15222635	D347	Jacob Tennessen	Burkina Faso	Tengrela	2016	-1	10.700	-4.800	F	...	Cascades	BF-02	Comoe	coluzzii	BF-02_colu_2016	BF-02_colu_2016	BF-02_colu_2016	BF-02_Comoe_colu_2016	BF-02_Comoe_colu_2016	BF-02_Comoe_colu_2016
19770	SAMN15222636	D348	Jacob Tennessen	Burkina Faso	Tengrela	2016	-1	10.700	-4.800	F	...	Cascades	BF-02	Comoe	coluzzii	BF-02_colu_2016	BF-02_colu_2016	BF-02_colu_2016	BF-02_Comoe_colu_2016	BF-02_Comoe_colu_2016	BF-02_Comoe_colu_2016

1757 rows × 57 columns

Example query to combine with other filters:

df_samples.query("country == 'Burkina Faso' and unrestricted_use")

	sample_id	partner_sample_id	contributor	country	location	year	month	latitude	longitude	sex_call	...	admin1_name	admin1_iso	admin2_name	taxon	cohort_admin1_year	cohort_admin1_month	cohort_admin1_quarter	cohort_admin2_year	cohort_admin2_month	cohort_admin2_quarter
19466	SAMN03299607	GOUND_0022	Jacob E Crawford	Burkina Faso	Goundry	2008	11	12.518	-1.341	UKN	...	Plateau Central	BF-11	Oubritenga	arabiensis	BF-11_arab_2008	BF-11_arab_2008_11	BF-11_arab_2008_Q4	BF-11_Oubritenga_arab_2008	BF-11_Oubritenga_arab_2008_11	BF-11_Oubritenga_arab_2008_Q4
19467	SAMN03299611	GOUND_0103	Jacob E Crawford	Burkina Faso	Goundry	2008	11	12.518	-1.341	F	...	Plateau Central	BF-11	Oubritenga	arabiensis	BF-11_arab_2008	BF-11_arab_2008_11	BF-11_arab_2008_Q4	BF-11_Oubritenga_arab_2008	BF-11_Oubritenga_arab_2008_11	BF-11_Oubritenga_arab_2008_Q4
19468	SAMN03299612	GOUND_0105	Jacob E Crawford	Burkina Faso	Goundry	2008	11	12.518	-1.341	UKN	...	Plateau Central	BF-11	Oubritenga	arabiensis	BF-11_arab_2008	BF-11_arab_2008_11	BF-11_arab_2008_Q4	BF-11_Oubritenga_arab_2008	BF-11_Oubritenga_arab_2008_11	BF-11_Oubritenga_arab_2008_Q4
19469	SAMN03299614	GOUND_0137	Jacob E Crawford	Burkina Faso	Goundry	2008	11	12.518	-1.341	F	...	Plateau Central	BF-11	Oubritenga	arabiensis	BF-11_arab_2008	BF-11_arab_2008_11	BF-11_arab_2008_Q4	BF-11_Oubritenga_arab_2008	BF-11_Oubritenga_arab_2008_11	BF-11_Oubritenga_arab_2008_Q4
19470	SAMN03299615	KODOU_0009	Jacob E Crawford	Burkina Faso	Kodougou	2008	11	12.520	-3.607	F	...	Boucle du Mouhoun	BF-01	Kossi	arabiensis	BF-01_arab_2008	BF-01_arab_2008_11	BF-01_arab_2008_Q4	BF-01_Kossi_arab_2008	BF-01_Kossi_arab_2008_11	BF-01_Kossi_arab_2008_Q4
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
19766	SAMN15222632	D342	Jacob Tennessen	Burkina Faso	Tengrela	2016	-1	10.700	-4.800	F	...	Cascades	BF-02	Comoe	coluzzii	BF-02_colu_2016	BF-02_colu_2016	BF-02_colu_2016	BF-02_Comoe_colu_2016	BF-02_Comoe_colu_2016	BF-02_Comoe_colu_2016
19767	SAMN15222633	D343	Jacob Tennessen	Burkina Faso	Tengrela	2016	-1	10.700	-4.800	F	...	Cascades	BF-02	Comoe	coluzzii	BF-02_colu_2016	BF-02_colu_2016	BF-02_colu_2016	BF-02_Comoe_colu_2016	BF-02_Comoe_colu_2016	BF-02_Comoe_colu_2016
19768	SAMN15222634	D346	Jacob Tennessen	Burkina Faso	Tengrela	2016	-1	10.700	-4.800	F	...	Cascades	BF-02	Comoe	coluzzii	BF-02_colu_2016	BF-02_colu_2016	BF-02_colu_2016	BF-02_Comoe_colu_2016	BF-02_Comoe_colu_2016	BF-02_Comoe_colu_2016
19769	SAMN15222635	D347	Jacob Tennessen	Burkina Faso	Tengrela	2016	-1	10.700	-4.800	F	...	Cascades	BF-02	Comoe	coluzzii	BF-02_colu_2016	BF-02_colu_2016	BF-02_colu_2016	BF-02_Comoe_colu_2016	BF-02_Comoe_colu_2016	BF-02_Comoe_colu_2016
19770	SAMN15222636	D348	Jacob Tennessen	Burkina Faso	Tengrela	2016	-1	10.700	-4.800	F	...	Cascades	BF-02	Comoe	coluzzii	BF-02_colu_2016	BF-02_colu_2016	BF-02_colu_2016	BF-02_Comoe_colu_2016	BF-02_Comoe_colu_2016	BF-02_Comoe_colu_2016

243 rows × 57 columns

Note that all sample sets in the vector observatory can be accessed and analysed at any time for public health purposes. If any terms of use apply, they may restrict the public communication of any analysis results (publication embargo) for a period of time.

If you have any questions about usage restrictions, please get in touch via support@malariagen.net.