environmentontology / gaz

An open source gazetteer constructed on ontological principles

GAZ

An open source gazetteer constructed on ontological principles.

• Creator: Michael Ashburner (retired)
• Lead-editor: Lynn Schriml (caretaker -- coordinating community efforts)

Brief description

GAZ is a large, ontologically-oriented resource listing place names which can be treated as instances of environments (see ENVO).

Getting GAZ

Due to size constraints, GAZ's OWL- and OBO-formatted files will not be hosted here for the moment. You can, however, download them here:

• GAZ in OWL format ca. 600 MB
• GAZ in OBO format ca. 180 MB

##GitHub can handle large files, extension git-lfs extension [Download] (https://git-lfs.github.com)

Issues, comments, and questions

Please use this repository's issue tracker to post issues (such as new term requests), comments, and questions.

gaz's Issues

NRTs: 'Earth (planet)' ... or 'globe'

We restrict ourselves to GAZ for geographic locations, but frequently bump into the problem of GAZ lacking a global term. Some suggestions:

term: Earth (planet)
mirror from: http://purl.obolibrary.org/obo/OMIT_0018724

term: globe [or, possibly, 'global', though using an adjective doesn't fit with other GAZ terms]

Upload all of GAZ to wikidata

We don't have resources to update gaz.obo. Unless we can find a volunteer it may make most sense to upload to wikidata and have people update on wikidata (having a way to export a gazetteer in obo or owl from wikidata will be easy).

If people are in favor I can look to getting some tips on how best to do this

GAZ should not import "environmental system process" or "environmental material" and subclasses.

GAZ is importing lots of ENVO, which is importing lots of FOODON?
See http://www.ontobee.org/ontology/GAZ?iri=http://purl.obolibrary.org/obo/FOODON_00002451

Publish subsets aligned to official naming schemes

Particularly for country names, several groups publish official names that must be used (e.g. UNGEGN, the UN itself, referencing ISO etc).

GAZ should probably have an AP for "UN official name" etc, populated with these values.

We can then export OWL/JSON-LD files for each official list, with the official name as the primary label, the relevant codes if any, and the GAZ IRI.

How to cite?

Greetings, I am interested in citing Gazeteer in a manuscript. Can you point me towards a publication or some other artifact you'd like me to cite to? Thank you.

Elizabeth Umberfield, PhD, RN
Postdoctoral Research Fellow
Public & Population Health Informatics
Regenstrief Institute and Indiana University Fairbanks School of Public Health
[email protected]

Zip code ZCAT and geographic coordinate

I am new to the GZ but I have recently start working on geospatial data and one of the issue I am having is the following
The data I am working on are capturing the zip code information but as you know this is a label for postal service and does not have any direct relation with the ZCAT and the geographic coordinates.
Is this the right place to raise this issue?

Marine Regions Gazetteer

Question migrated over from #23

Perhaps lower priority issue for now, but do you think there could be any scope to link GAZ to the Marine Regions Gazetteer it's a pretty extensive resource which has term hierarchies for Large Marine Ecosystems of the World, Longhurst Provinces etc. This could be quite a useful resource for the Oceans and Seas module.

Determine who is using GAZ and how it is being used

Anyone using GAZ, please add comments to this ticket!

Also include whether you use the obo or owl file, if you download or use an API, etc. Note any specific things you would like to see at a general level (or link to a ticket)

Ensure non-ascii form of names are present (e.g. umlauts, as in Gurbantünggüt desert)

Searching OLS for Gurbantünggüt desert returns no results

The term in GAZ is "Gurbantunggut Desert"

https://www.ebi.ac.uk/ols/ontologies/gaz/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGAZ_00114666

Perhaps the OLS should be enhanced to better be able to search on umlauts

But either way the official name seems to have umlauts, GAZ should have them

I imagine there were issues with umlauts in obo-edit

We could look to correcting these automatically once wikidata xrefs are done, as WP/WD has the formal name: https://en.wikipedia.org/wiki/Gurbant%C3%BCngg%C3%BCt_Desert

Random fact:

t is in this desert that the remotest point of land from any sea is located. According to some calculations, the precise point is at 46°16.8′N 86°40.2′E. It was pinpointed and reached on 27 June 1986 by British explorers Nicholas Crane and Richard Crane; the location was described as being in the Dzoosotoyn Elisen Desert. This position is over 2,600 kilometers (1,600 mi) from the nearest coastline.[5]

It would be neat to have this point in GAZ but we have no use case for this...

Rename South Africa GAZ:00000553

I would like to request this term is renamed as
'Southern Africa' GAZ:00000553
to avoid confusion with the country commonly known as 'South Africa'.

If it's not possible to rename this, suggest adding Southern Africa as a synonym.

Thanks,
Varsha

Biogeographic regions

Hi @EnvironmentOntology/gaz-editors , branching from #20:

While GAZ was dormant, we incubated a few WWF ecoregions in ENVO. See EnvironmentOntology/envo#658

When you get to those modules, let us know and we'll obsolete our instances and point to GAZ instances.

As ENVO is meant to provide the classes for GAZ's instances, do let us know if you need more content ENVO side. You're also welcome to propose edits yourselves.

Proposal: convert GAZ to an instance-based representation

Currently GAZ is represented as all classes. E.g. Andorra is a class. Clearly this is not correct, but it's well-known that the reason for this choice is purely pragmatic - Michael would edit in Obo-Edit, which only handles classes.

I propose the following:

• gaz.owl is converted to an instance-based representation
• gaz.obo is converted to classes in the release process (instances are not well-supported in .obo format)

Any consumers of gaz.obo (which includes a number of relational database systems) should be unaffected, provided the conversion does not lose anything.

We would also need to check with all consumers of gaz.owl to make sure this does not break anything.

I think the OLS display would break somewhat, but we can just point OLS at gaz.obo

This will need considerable planning.

• Will editing instances in Protege be as easy as editing classes? The current representation of GAZ is not just geared towards OE, it's an easy structure to browse (especially now Protege supports existential hierarchies directly)
• We will need at least preliminary rdf:type / ClassAssertion axioms, I had a conversion at some point, will look this up...

Add obofoundry topic to repo metadata

The OBO Foundry has recently created a topics page at https://github.com/topics/obofoundry. It would be great if you could add the obofoundry topic to your repository, since it's currently listed as active in the OBO Foundry. If you're not sure how to do that, follow the instructions here. The main issue for this task is at OBOFoundry/OBOFoundry.github.io#1538 in case you want some more context or to join the larger discussion.

USA and many other GAZ terms are classes & instances simultaneously

It appears that many GAZ terms like "USA" (http://purl.obolibrary.org/obo/GAZ_00002459) and "geographic location" (http://purl.obolibrary.org/obo/GAZ_00000448) are defined as both classes and instances. This may not be correct.

Explanatory document for newbies

GAZ needs an explanatory document for newbies – how to get a country's 2nd level subdivisions, whether they are states/provinces/territories/regions etc. and the linkage between geopolitical levels of government entities using "located in". Same for municipalities, villages, ENVO human habitation etc… Unless there is some documentation about this that I don't know about?

NTR: North Sea coastal waters of Belgium

Suggest new term
"North Sea coastal waters of Belgium"

as sibling of
North Sea coastal waters of Norway GAZ:00144350
North Sea coastal waters of Denmark GAZ:00144351
North Sea coastal waters of the United Kingdom GAZ:00144349

Thanks,
Varsha

Update OBOFoundry home page link for GAZ tracker

Currently it is pointing to the ENVO issues list rather than the new GAZ location:
https://github.com/EnvironmentOntology/gaz/issues

Add synonym to GAZ:00001099

Add synonyms 'Eswatini' and 'Kingdom of Eswatini' to GAZ:00001099 (Swaziland): https://en.wikipedia.org/wiki/Eswatini

Alternatively, rename this term to 'Eswatini'.

Decide how to modularize GAZ such that individual subsets can be managed in github

• What source format? .obo is easy for diffing but this assumes we don't convert to instances. Dependency on #20
• How do we modularize? We need a set of mutually exclusive exhaustive categories. If this is not possible we need an agreed upon prioritization to detemine which entity belongs in which module
• How do we determine the initial conversion is not lossy?
  • robot diff doesn't scale
  • If we punt on #20 for now, then obo-level diffing is very easy and scalable, could be done at the ascii level even, I also have scripts here: https://github.com/cmungall/obo-scripts
  • for an instance representation, there will be no blank nodes so this makes RDF-level diffing easy

GAZ is inconsistent

In an attempt to set up a uniform set of quality control checks across OBO ontologies, we noticed that GAZ is currently inconsistent. Due to its size, its a bit hard to determine run the reasoner in protege, so here the explanation for the inconsistency:

Thing SubClassOf Nothing

Reason for inconsistency:

grassland area is ultimately classified as an immaterial entity:

• site SubClassOf immaterial entity
• environmental zone SubClassOf site
• terrestrial environmental zone SubClassOf environmental zone
• vegetated area SubClassOf terrestrial environmental zone
• grassland area SubClassOf vegetated area

undersea feature is ultimately classified as a material entity

• fiat object part SubClassOf material entity
• astronomical body part SubClassOf fiat object part
• geographic feature SubClassOf astronomical body part
• hydrographic feature SubClassOf geographic feature
• undersea feature SubClassOf hydrographic feature

Nothing can be both material and immaterial

• material entity DisjointWith immaterial entity

Tualatin Mountains are instances of both of the above.

• Tualatin Mountains Type undersea feature
• Tualatin Mountains Type grassland area

Which seems to come from a bad interaction between ENVO and GAZ. This may not solve the deeper modelling issue, but at least could drastically reduce the error severity: removing the type assertions on Tualatin Mountains.

NTR: Ankeniheny-Zahamena Corridor

NTR: Ankeniheny-Zahamena Corridor
Defn: links Zahamena National Park (GAZ:00076565) and Andasibe-Mantadia National Park (GAZ:00005428)

NTRs: names for experimental field sites

From EnvironmentOntology/envo#601

@richardostler requested some guidance on adding instances for "experimental field".

@richardostler Could you list the names of these sites here and some definitions regarding their location and boundaries?

@lschriml we'll add the general class for "experimental field" to ENVO under which the GAZ instances can be placed after their created.

GAZ national populated place classes should cover municipalities?

For example, GAZ "populated place, Brazil" http://purl.obolibrary.org/obo/GAZ_00002831) lists 35 places, while https://en.wikipedia.org/wiki/Municipalities_of_Brazil lists 5,570 municipalities.

Perhaps a wikidata integration could resolve this, or a geonames integration? Our use case is that we have some dynamic lookup trying to fetch the municipality for a user to specify a biosample location.

Replace obsolete 'lava field' (ENVO:00000095)

Replace old ENVO:00000095 with new ENVO:01000437 (also lava field).

It's currently in use in the following country subsets (which I'll be pushing shortly):

• Canada
• Guatemala
• Nicaragua
• United States of America

Evaluate coverage of GAZ with respect to other resources

We are currently aligning to wikidata (#3)

It would be useful to see a complete landscape picture of what is covered and not covered in existing resources, alongside any licensing restrictions.

This can help us with prioritizing curation resources - no need to redo what is there in an existing open resources

geonames seems to be CC-BY, so would be no issue in re-using

They have a premium tier but I don't think we need it
http://www.geonames.org/products/premium-data.html

Cross-ticket on RDP: reusabledata/reusabledata#185

Geographic relations

Hi all, branching off of #21

GAZ will inevitably need some more geographically themed relations in RO, linked to issues such as
EnvironmentOntology/envo#80, EnvironmentOntology/envo#148

Many existing spatial relations coming in from biology and anatomy can be used if their definitions are generalised a bit or if more general superclasses are created.

@rctauber @cmungall @lschriml Shall we use this issue to log object properties that GAZ curators feel would be useful?

GAZ hasDbXref to ISO_3166 countries

GAZ offers up these database cross references for, e.g. Belgium

"hasDbXref": [
"ISO3166-1:BE",
"ISO3166-2:BE",
"ISO3166-1:BEL",
"ISO3166-1:056"
]
But there are actually sub-categories of ISO3166-1, and that's why what looks like a 1-many mapping is actually 1-1 if subcategory is taken into account. I'm not sure how exactly to represent it but something like?

hasDbXref 
  https://www.iso.org/obp/ui/#iso:code:3166:BE
  ISO_3166-1_alpha-2:BE
  ISO_3166-1_alpha-3:BEL
  ISO_3166-1_numeric:056
  ISO_3166-2:BE

More info at:
https://en.wikipedia.org/wiki/ISO_3166

Some related work: https://arxiv.org/pdf/0801.3908.pdf
https://www.slideshare.net/nichtich/encoding-changing-country-codes-in-rdf-with-iso-3166-and-skos

Module priority: Oceans and seas

Related to #4

@rctauber @lschriml : It would be fantastic if modules for oceans and seas could be released.
We'd readily use them in the UNESCO/IOC Ocean Best Practices System: www.oceanbestpractices.org

Transitioning from GAZ to Wikidata - is there a comprehensive query?

As a transition effort from GAZ to wikidata, I will try to figure out a comprehensive wikidata query that can retrieve all continents and countries of the world, and their states/provinces/territories, cities/towns/villages but before I start, has any GAZ curator already done this? I don't need the map from GAZ to Wikidata ID's - just the Wikidata hierarchy of things. [EDIT: this would be used to create a dynamic menu system to aid in data entry, providing picklists for users. Its not good UI just to dump users over in wikidata to search for a town etc.]

Identify Wikidata reconciliation strategies for GAZ.

GAZ does seem to have many mappings to external identifiers (if at all). This makes aligning Wikidata particularly challenging.

To get all terms in GAZ covered in Wikidata we would probably need to apply different strategies to see if a term is already is covered or not.

In the case where the label used in Wikidata exactly matches the term in GAZ, Open refine, can be our friend. I used this tool - offered in for example PAWS - to align GAZ countries with Wikidata.

However, I continued with terms on Suriname in GAZ. So far all terms do exist in Wikidata but most with a different spelling variation. I will try to add all GAZ terms for that country, manually.

So so far two strategies have been applied:

1. Where the terms match exactly in Wikidata, we can rely on Open Refine
2. Where the terms exist, but with difference in spelling, manual curation by a curator with local knowledge is required
3. .......

GAZ to INSDC country list mapping

In an effort to comply with INSDC reporting of sample location by country, we have created a mapping of GAZ country & region codes to their INSDC counterparts at http://www.insdc.org/country.html by using a hasDbXref:INSDC:country:[xyz] annotation on the appropriate GAZ item. Is the GAZ team interested in adding these annotations directly to GAZ? If so we have the .owl import file containing the annotations we can provide that could be easily merged.

The include file is at https://github.com/GenEpiO/genepio/blob/master/imports/gaz_insdc_mapping.owl
see
http://www.insdc.org/country.html
It is based on https://unstats.un.org/unsd/methodology/m49/ , but sadly, in either case, there are no region / country-specific purls to offer.

do we need GAZ?

I don't understand why we need an ontology for this when other standards like geonames already exist. I view it more like the issues with making gene names available for axioms.

Coordinating and Prioritizing tasks for GAZ

I would like to plan a meeting of the GAZ group, to prioritize
tasks and to determine who will carry out the work, and take
responsibility for the various tickets.

Please indicate your availability in this ticket, so that we can coordinate a call for
early June.

Lynn: On travel May 15-29, fairly open schedule first two weeks of June.

Cheers,
Lynn

How confident is "high" in https://raw.githubusercontent.com/INCATools/environments2wikidata/master/matches/align-high-confidence-gaz.tsv

I stumbled upon this table.

Can I assume the identifiers for these GAZ terms can be added to Wikidata without further validation?

Also, can I read "c1parent" as rdfs:subclass of?

New Regional division in Norway

Norwegian region system has been remodeled in 2020. Here is the new regional divisions:
https://en.wikipedia.org/wiki/Counties_of_Norway

GAZ license

Looks like in this repo and in the OBO metadata GAZ is asserted to be CC-BY:

OBOFoundry/OBOFoundry.github.io@27de032#diff-55585add55c612de501c3934421cb36c
(wasn't part of a PR or issue)

I think this requires further discussion

GAZ "JIle uan de Nova" label needs fix

"JIle uan de Nova" label for http://purl.obolibrary.org/obo/GAZ_00005809 should be "Ile Juan de Nova". http://en.wikipedia.org/wiki/Juan_de_Nova_Island

Catalog all uses of GAZ

We should catalog all uses of GAZ. This should be limited to actual documented verifiable uses (but it would also be good to collect broader requirements in a google doc)

For details of the format, see the usages field here:

https://raw.githubusercontent.com/OBOFoundry/OBOFoundry.github.io/master/ontology/envo.md

Request GAZ class "State (United States of America)"

GAZ has state classes for Mexico, Australia etc. Can we get this for the US to provide easy menu selection? Wikipedia def seem fine:

label: "State (United States of America)"
definition: "In the United States, a state is a constituent political entity, of which there are currently 50. Bound together in a political union, each state holds governmental jurisdiction over a separate and defined geographic territory and shares its sovereignty with the federal government."
definition source: https://en.wikipedia.org/wiki/U.S._state

If helpful, SPARQL query is in "insert USAstate" query in https://github.com/GenEpiO/genepio/blob/master/src/ontology/gazetteer2.py , although I see a few american protectorates in there too, and it uses GenEpiO's "US state" class.

Also, there is one discrepancy in Gazetteer right now:
It had adopted the practice of having owl:NamedIndividual with same id's as owl:Class for a number of items (punning), but not for states in the USA.

Marking countries like Yugoslavia as historic/archaic

In order to avoid including archaic nations in a "nation" selection list, we need an object property for marking them as such, perhaps using "instance of" "historical country" as wikidata does?

Create unique names for entities

A long time ago I had a discussion with Michael about entity names. GAZ stood in contrast to everything else in OBO that had largely unique names.

He convinced me that it was fine in GAZ to have many entities in GAZ share the same name. However, it might be nice to create a unique obo foundry unique label for all entities.

An important note that will hopefully become stale soon. In previous versions of Protege, you get into massive trouble if your ontology has entities that share the same rdfs:label. I think this is fixed in 5.5 or 5.6 but haven't tested. This should probably be in the editor docs when we get them up

Create GAZ webpages

Cross-reference EnvironmentOntology/envo#313.
Centralise any GAZ descriptions and material here.
An initial landing page is available at: http://environmentontology.github.io/gaz/