Control strategy

[LucieContamin]

• add control strategy and prion
• minor update

fixes #92 , #93 , #91 , #94

[harryhoch]

is this a request for a review?

[LucieContamin]

Sorry for the confusion, is just to go with the issue #94, I will keep it open until revision. It contains the same information.

[harryhoch]

ok

[LucieContamin]

Can I keep it open as a draft maybe to avoid confusion but to have the branch open for update and revision?

[harryhoch]

that's fine.

[LucieContamin]

Here a summary of all the updates in the current PR, the column "change" indicate any change in the control strategy topics (new, move to a new tier, deprecated (noted removed in the table)). I also have some open question in the Notes column:

The issue #99 , is also still ongoing and I will update the PR once resolved.

Change	Level0	Level1	Level2	Level3	Level4	Level5	Definition	IRI	Notes
	topic						The subject of the digital object - what it is about.	http://w3id.org/midas-metadata/midas2
		control strategy census					a census of infectious disease control strategies put into place to reduce infection acquisitions that are part of an infection in an ecosystem.	http://purl.obolibrary.org/obo/APOLLO_SV_00000604
			school closure control strategy census				an infectious disease control strategy census that is about school closure infectious disease control strategies implemented in a particular geographical region.	http://purl.obolibrary.org/obo/APOLLO_SV_00000605
NEW			population treatment census				A census about a particular medical treatment of a population	http://purl.obolibrary.org/obo/APOLLO_SV_00000187	Does this one match with the associated strategy of individual treatment (http://purl.obolibrary.org/obo/APOLLO_SV_00000194)? I am not certain it matches but I cannot find another census strategy in Apollo
NEW				antibody administration census			a population treatment census that is about one or more antibodies administrations of organisms in a population		Can we ask that one to be added to Apollo?
MOVE				vaccination administration census			a population treatment census that is about one or more vaccinations of organisms in a population	http://purl.obolibrary.org/obo/APOLLO_SV_00000607
MOVE					cumulative vaccination count		A count of vaccinations in a population that is the total number of a given type of vaccines administered during a reference temporal interval.	http://purl.obolibrary.org/obo/APOLLO_SV_00000640
MOVE					incident vaccination count		A count of vaccinations in a population that is the number of a given type of vaccines administered during a proper occurrent part of a reference temporal interval.	http://purl.obolibrary.org/obo/APOLLO_SV_00000641
MOVE			census of vaccination supplies				A control strategy inventory census that counts available vaccine doses of one or more similar vaccines.	http://purl.obolibrary.org/obo/APOLLO_SV_00000609
MOVE			vaccination administration capacity				An action specification giving the number of vaccinations possible in a population during a specific time interval.	http://purl.obolibrary.org/obo/APOLLO_SV_00000047
			laboratory testing capacity				An action specification giving the number of laboratory tests of a certain type that it is possible to perform in a given population during a specific time interval.	http://purl.obolibrary.org/obo/APOLLO_SV_00000613
			laboratory testing facility census				A census of facilities that conduct clinical laboratory testing.	http://purl.obolibrary.org/obo/APOLLO_SV_00000610
NEW		infectious disease control strategy					A plan specification whose objective specification is an infectious disease control objective specification.	http://purl.obolibrary.org/obo/APOLLO_SV_00000086
NEW			contact tracing				An infectious disease control strategy that identifies and treats contacted organisms in a host population.	http://purl.obolibrary.org/obo/APOLLO_SV_00000550
MOVE			event cancellations				Events that were cancelled due to an outbreak	http://w3id.org/midas-metadata/midas45
NEW			Hand Hygiene				Practices involved in preventing the transmission of diseases by hand.	http://id.nlm.nih.gov/mesh/D063373	Cannot find a good definition for that one - find a mesh term, is that accepted?
NEW			individual treatment control strategy				An infectious disease control strategy that immediately targets individuals.	http://purl.obolibrary.org/obo/APOLLO_SV_00000194
NEW				anti-infective individual treatment control strategy			An individual treatment control strategy that has as part an action specification that is realized in anti-infective treatment.	http://purl.obolibrary.org/obo/APOLLO_SV_00000304
NEW				vaccination control strategy			An individual treatment control strategy that has as part an action specification that is realized in a vaccination process.	http://purl.obolibrary.org/obo/APOLLO_SV_00000136
NEW				antibody control strategy			An individual treatment control strategy that has as part an action specification that is realized in an antibody injection process.		Can we ask that one to be added to Apollo?
NEW			Personal Protective Equipment				Masks, shields, gloves, gowns, boots, or other equipment used to provide coverage against infectious agents or environmental hazards.	http://purl.obolibrary.org/obo/NCIT_C173748
NEW				Protective Face Mask			A barrier device that covers the nose and mouth, used in infection control.	http://purl.obolibrary.org/obo/NCIT_C173747
NEW			place closure control strategy				An infectious disease control strategy that has an action specification that is realized in closing facilities where organisms congregate during times when the facilities normally would be open.	http://purl.obolibrary.org/obo/APOLLO_SV_00000229
NEW				close individual places independently strategy			A place-closure control strategy that decides on a case-by-case basis whether to close places of a certain type, as opposed to blanket policy that closes all places of a certain type at the same time.	http://purl.obolibrary.org/obo/APOLLO_SV_00000286
NEW				lockdown infectious disease control measure			A place closure control strategy in which only selected places in a geographical region are permitted to stay open and travel is permitted only for people employed by certain organizations.	http://purl.obolibrary.org/obo/APOLLO_SV_00000621
NEW				school closure control strategy			A place closure control strategy whose action specification is realized in a school closure process.	http://purl.obolibrary.org/obo/APOLLO_SV_00000123
NEW			quarantine				Place into enforced isolation	http://purl.obolibrary.org/obo/NCIT_C71902
NEW				voluntary household quarantine control strategy			An infectious disease control strategy whereby the household members of infectious indivduals voluntarily stay at home to avoid further potentially infectious contacts.	http://purl.obolibrary.org/obo/APOLLO_SV_00000322
NEW			Screening Test				A test whose operational purpose is to determine the presence or absence of a substance, organism, or condition.	http://purl.obolibrary.org/obo/NCIT_C181548
NEW			Social Distancing				The practice of keeping a safe space between yourself and other people.	http://purl.obolibrary.org/obo/NCIT_C173636
NEW			travel-related infectious disease control strategy				An infectious disease control strategy that has an objective specification of preventing infection acquisition by organisms traveling from one ecosystem to another ecosystem.	http://purl.obolibrary.org/obo/APOLLO_SV_00000486
NEW				border control strategy			A travel-related infectious disease control strategy that has an action specification that is realized in restricting movement of organisms across international borders.	http://purl.obolibrary.org/obo/APOLLO_SV_00000228
NEW				travel restriction control strategy			A travel-related infectious disease control strategy whose action specification is realized in restricting travel of organims from one ecosystem to another ecosystem	http://purl.obolibrary.org/obo/APOLLO_SV_00000231
NEW				travel recommendation control strategy			A travel-related infectious disease control strategy that has an action specification that is realized by making recommendations to travelers to either (1) avoid travel to an ecosystem with an ongoing infection such as an epidemic, (2) take precautions when traveling to such an ecosystem, (3) receive certain vaccinations prior to traveling to such an ecosystem, or (4) take certain medications when traveling to such an ecosystem	http://purl.obolibrary.org/obo/APOLLO_SV_00000487
NEW			vector control strategy				An infectious disease control strategy that has a vector control action specification as part.	http://purl.obolibrary.org/obo/APOLLO_SV_00000308
MOVE			Wildlife Health Interventions				A range of activities focused on preventing, managing, and mitigating health issues in wild animal populations, including disease prevention, public health considerations, etc.	http://w3id.org/midas-metadata/midas92
		media					Information about media, coverage about a topic	http://w3id.org/midas-metadata/midas74
NEW			Media Campaign				Public communication via television, radio, newspapers, pamphlets, telephone, and other media to influence health or social behaviors.	http://purl.obolibrary.org/obo/NCIT_C18227
			social media				Datasets discussing outbreaks on social media sites	http://w3id.org/midas-metadata/midas85
MOVE		regulatory complaints					Reports of policy violations	http://w3id.org/midas-metadata/midas62
MOVE		risk factors					Aggregate descriptions of multiple factors invovling susceptibility to outbreaks	http://w3id.org/midas-metadata/midas57
	REMOVED
REMOVED			drug treatment	replace by anti-infective treatment			A treatment with a drug product.	http://purl.obolibrary.org/obo/APOLLO_SV_00000318
REMOVED			vaccination with nirsevimab	replace by antibody control strategy			A vaccination against respiratory syncytial virus via the administration of the monoclonal antibody nirsevimab	http://purl.obolibrary.org/obo/APOLLO_SV_00000639
REMOVED			vaccination	replace by vaccination control strategy			A treatment that consists of the administration of antigenic material to stimulate an individual's immune system to develop adaptive immunity to a pathogen.	http://purl.obolibrary.org/obo/APOLLO_SV_00000142

[harryhoch]

I will try to look at this tomorrow, but it looks very thorough and impressive - thanks!

[harryhoch]

@LucieContamin, this looks very good.

One minor comment. Population treatment Census. You asked how it algns with individual treatment control strategy. I think the two things are quite different.

For one, population treatment census is a count, while individual treatment control strategy is a concept. This gets back to the difference between "X" and "census of x". These should be distinct.

The other issue is that individual treatment control strategy is designed to be aiming at individual persons. If you look at its parent - infectious disease control strategy , you'll sae lots of control strategies, many of which are population level, so this one stands out as being individual.

I assume we'll keep open until #99 is addressed?