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If an issue here gets large, start an separate topic and link it here.

See also [[PlaziFinalReport]] for issues identified by the [[PlaziEOLProject]]

* [[Concept of Descriptions]] - What are descriptions? Is Behavior or DNA sequence not a description? But physiology, anatomy, chemistry, morphology are?

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* Recommended Instance Form: Should an instance document be valid OWL?

I think yes. It makes it easier to write robust applications. On the other hand, it needs usable tools... -- Main.BobMorris - 09 May 2007

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* Rendering Instance Documents: What are the recommended tools for rendering instance documents? Does this depend on the above? -- Main.BobMorris - 14 May 2007

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* Repeated targets of the same hasInformation: Suppose an info item, say Range, has multiple values, e.g. representing that the range of a certain species includes Germany, France, and Belgium. Does this require three hasInformation triples (I suppose the answer is yes) and how do we guarantee that they are all talking about the same thing (I suppose the answer is use owl:sameAs). -- Main.BobMorris - 20 Jul 2007

---++Issues and Questions from PlaziFinalReport

Below we discuss 12 issues that Plazi faced during the development, including what we did about them and what recommendations we have based on our experiences.&nbsp; Some of these issues are not about SPM per-se except to the extent we found ambiguities or silence in SPM. Some may be addressed in the recent GBIF draft recommendations on&nbsp; the (<i>Cryer, et. al 2009 Adoption of Persistent Identifiers for Biodiversity Informatics</i>, http://imsgbif.gbif.org/File/retrieve.php?PATH=4&amp;FILE=2efc20187e6ad3dd828bbeadaa1040e6&amp;FILENAME=LGTGReportDraft.pdf&amp;TYPE=application/pdf)<br>

*Issue 1*. Validation of the RDF to ensure RDF being produced was valid. This was accomplished by testing against the web-based [[http://www.w3.org/RDF/Validator/ !W3C RDF validator]]. We found this a particularly useful tool since it yields easy to understand representations of the RDF triples generated. By contrast, easy as the XML form of RDF is for humans to read, it is not always easy to understand from it whether one or another RDF predicate is being correctly or appropriately used.

_Conclusions and Recommendations about Issue1:_

Best practices for ontology annotation should be developed, perhaps with particular attention to documenting predicates.<br>

*Issue 2.*Even for valid RDF there was still a question as to whether it was valid OWL RDF, or whether OWL RDF was a goal.

No clear goals have been set and documented by GBIF or TDWG about reasoning on SPM, or other TDWG ontology vocabularies. It is generally accepted that the OWL Full dialect of OWL promotes data integration robustly in the sense that OWL Full has enough expressiveness to give integrators confidence in semantic equivalences or near equivalences in their mappings between one vocabulary and another. However, the OWL DL (Description Logics) dialect of OWL promotes tractable&nbsp; reasoning computation, making it easier to determine, e.g. whether a pair of vocabularies are logically inconsistent with one another, or whether data violates some quality control axioms that an application might wish to enforce. SPM invokes quite a bit of the current TDWG ontology, with the consequence that SPM is OWL FULL but not DL, because some of the TDWG ontology is not.

The "Open World" assumption for RDF is presently frequently cited as the slogan "AAA" (Anyone can say Anything Anywhere). One consequences is that misuses of ontology constructs can inadvertently pass into instances (by instance generation code), without discovery merely by RDF validation.&nbsp; This can happen if known applications do not fail on the misuse because it addresses issues the application ignores, or because particular consequences are harmless (e.g. because they return empty resource URI's and so are about nothing). One such SPM instance generation error was discovered only at the time of this writing in trying to understand why the Manchester !WonderWeb OWL validator ( http://www.mygrid.org.uk/OWL/Validator) was asserting that _!TaxonConcept_ was being used as both an RDF Class and an RDF Property. That is forbidden in OWL DL, but not OWL Full, for which the SPM instances were valid OWL. No such invalidity appeared in either the SPM ontology or the TDWG Ontology. The problem proved to be that the Plazi XSLT was generating incorrect RDF for the _hasRelationship_ object property of _TaxonConcept_ where it expected a Relationship object, which is one of the low level classes in the TDWG ontology.

We were intending to model not only what taxa were associated with the

_!TaxonConcept_ being described&nbsp; (as supported by SPM

_!InfoItems_), but also what those associations are. (The SPM

annotations give predator-prey relationships as an example.) The

result was that the instance document used _TaxonConcept_ as both a

Property and a Class, and this forces the instance document into OWL

Full. Moreover, the underlying set of kinds of taxonomic relationships

available to _tc:hasRelationship_ is presently defined by an

enumeration that arose historically from a set of concerns of

taxonomists, largely about the nomenclatural issues surrounding

taxonomic revisions. This is nowhere near broad enough to cover the

kinds of _Associations_ envisioned in SPM, which includes such things

as predator/prey and other ecological relationships. Pending future

additions to !TaxonX, the underlying schema representing the documents

from which we extract SPM-based knowledge, we are no longer attempting

to output _tc:hasRelationship_.

_Conclusions and Recommendations about Issue 2:_

(1) The SPM concept _associatedTaxon_ is underspecified. It does not

provide a robust mechanism for specifying the nature of the

association. It is possibly that this can be remedied with a robust

appeal to _tc:hasRelationship_, although that presently has overly

narrow range.

(2) Clear goals for reasoning support for SPM should be elucidated.

*Issue 3a.* Some vocabulary items in SPMI lacked definition or guidance

for their use. For example, the SPMI ontology defines a set of

sublasses of the SPM _InfoItem_ class, of which one or more instances

is given for an SPM object using the _hasInformation_ property of

SPM. One such type of _InfoItem_ is the _Description. _But this term

is rather broadly used in biology. In systematics literature it is

ambiguous whether the concept should apply to the entire section

designated as the taxonomic treatment of a taxon in the article, or

should refer only to the morphological description section. By

practice or by nomenclatural codes, the morphological description

section serves, strictly speaking, only to determine which specimens

are circumscribed by that morphological description. We addressed this

ambiguity with a user-settable parameter in the stylesheet which

determines which of these is extracted. We offer a service parameter

that allows the client to determine whether they wish a narrowly(

i.e. morphology only) or broadly defined description.

*Issue 3b.* Insufficient SPMI concepts. Anyone providing data in SPM

faces a potential mismatch between domain concepts and those SPMI

classes they select to represent the domain classes. SPM can

address this by adding more types of _InfoItems_, but this will tend

to increase the complexity in creating and processing SPM. Conversely,

SPM could decrease the number of concepts and heighten ambiguity. For

example, we found no way to signal the important "Materials Examined"

section of typical systems papers. This might make it difficult to

mine our service for occurrence records.

*Issue 3c.* Potentially overlapping SPMI classes. There are three

different concepts in SPMI about description. These are the

_InfoItem_ subclasses _Description_, _GeneralDescription,_ and

_DiagnosticDescription._ Lacking definitions it is impossible to

determine what relations these have to one another.

_Conclusions and Recommendations about Issue 3: _

(1) There should be more guidance about the semantics of

_InfoItem_. Right now, they are little more than concept names. By

virtue of having no substructure other than what is inherited from

class _InfoItem_, these concepts are able to express little more than

the taxonomic concerns modeled by the class _TaxonConcept_, which are

probably of little importance for many of the subclasses of

_InfoItem_.

(2) Consideration should be given to major ontological elucidation of

the substructures of the InfoItem subclasses, with particular

attention to existing relevant ontologies.

*Issue 4.* Should text extracted from publications permit or require

markup? At the moment, we offer the choice as a runtime parameter, to

signify whether the service should return plain text or XHTML. Current

use for by EOL chooses the XHTML in order to render paragraph

boundaries faithfully to the original literature.

_Conclusions and Recommendations about Issue 4:_

We have no recommendation beyond leaving the issue as a service parameter.

*Issue 5.* How to handle statements of Intellectual Property

Rights. Taxonomic treatment data is in the public domain and not

copyrightable. EOL's practices required a Creative Commons license,

but such licenses (or any license) applies only to copyrightable

material. We insert an RDF statment a statement that the material has

no copyright restrictions:

<font face="Courier New">&lt;<span class=start-tag>dcterms:rights</span><span class=attribute-name> xmlns:dcterms</span>=<span class=attribute-value>"http://dublincore.org/2008/01/14/dcterms.rdf#"</span>&gt;</font>No known copyright restrictions.<font face="Courier New">.&lt;/<span class=end-tag>dcterms:rights</span>&gt;

</font>

We discussed whether more clarity is required about attribution of

non-copyrightable material. Should there be both a text statement

and a machine processable indication that the material is in the

public domain because it is not copyrightable? How should consumers

be warned that the non-copyrightable material is extracted from

copyrighted material which still requires attribution. The issues

are laid out in Agosti and Egloff (2009:

(http://www.biomedcentral.com/1756-0500/2/53). The current solution

to be adopted by EoL is to output the text mentioned above in our

dc:rights term.

*Issue 6. * Completeness and adequacy of data provided. It's unclear

how much detail the data provider should offer a data

recipient. For example, it may be evident to a human that the object

"Donisthorpe, H. S. J. K." of the _tpcit:authorship_ predicate is

the name of a person, that "Donisthorpe" is a surname, etc. This

semantics may be available through an ontology but not be of

interest if the recipient has no need of machine reasoning or even

integrating across authors. It's difficult to know at what point

enough information has been provided satisfy the data recipient's

purposes. We serve whatever data we found that is expressible in

the vocabularies commonly in use in TDWG applications.

_Conclusions and Recommendations about Issue 6:_

Educate consumers to the possibility that implict information can be

inferred by machine reasoning over the applicable ontologies, and

applications that don't do this can only have access to the explictly

asserted relationships.

*Issue 7.* Open World Issues. The Open World assumption (now often

described as the AAA slogan: Anybody can say Anything Anywhere )

means that some issues cannot be addressed by the data being served.

AAA means that everything is unknown unless explicitly known. Should

"unknown" be signaled in some cases? For example, a taxonomic

description might be extracted from something whose author is

unknown. Normally RDF would simply be silent on this point, but it

may be important to distinguish that a piece of data is important but

simply unknown. There is a risk in assigning "unknown" to something

which in fact is possibly somewhere known. That risk is that future

semantic data integration with data contradicting the "unknown"

semantics will then be logically inconsistent. Unfortunately, in the

First Order Logic that underlies RDF reasoning, if there is one

contradiction in a set of assertions, it can be proved that every

assertion is both true and false. This is not nice.

_Conclusions and Recommendations about Issue 7:_

Best practices should be established about unknown data. Probably the

community needs to be educated about AAA. A possible best practice

is to use RDF annotations when signifying "unknown" is desired.

These can be read by machines (and humans) but do not participate in

semantic analysis.

*Issue 8.* Updates: It is unclear how to handle URI's assigned to

different versions of the same SPM record. Should a URI resolve one

record regardless of what information is in it, or should each

version have it's own URI. Like most data providers, we largely

ignore this issue, although we do embed an XML comment with a service

timestamp on it.

_Conclusions and Recommendations about Issue 8:_

This is probably a general problem for RDF and should be the subject

of a uniform best practice. There is a recent GBIF workgroup report

on the subject. (Cryer et al. 2009)

*Issue 9.* Strings or URIs: As a data provider we sometimes faced the

choice of providing a URI or a string value for much of the data. In

principle, a URI should be sufficient but in practice it is helpful

to have both e.g., for scientific names. In the absence of guidance

from the data consumer it is impossible to know what is necessary or

sufficient. Other examples that SPM does not directly address, and

for which there seem to be no authorities presently recommended,

include URIs for taxonomies, ranks within those taxonomies, authors,

journals, articles, etc. Some of the issue is addressed by SPM's

provision of both _hasContent_ and _hasValue_ properties. The former

provides strings, and the latter provides objects from the TDWG

Ontology class _definedTerm_. The only case in which we might have

been able to use _definedTerm _would be to build some application

that attempts to place the publication's taxonomic rank in some

named taxonomy. We deemed that outside of the scope of this work,

particularly since a client might choose to ignore it and use their

own preferred taxonomy.

Elsewhere, we provide both strings and URIs where the publication is

unambiguous. See for example, the element _spm:aboutTaxon_ in the

first table above. For its target _!TaxonConcept_, we provide a

URI-identified rdf:about as required, but _!TaxonConcept _also has

an element _nameString_ with which we provide a string that should

correspond to a scientific name. An integrating provider such as EOL

possibly would choose to ignore the URI and base their integration

on the name string.

_Conclusions and Recommendations about Issue 9:_

Unless a consumer has specified preferences, whenever possible include

both string and URI values. It may be that best practices need to be

established for doing this in ways specific to SPM, or even to

individual SPMI _!InfoItems_.

*Issue 10:* Multiple identifiers: resources may have multiple ids in

multiple GUID schemes associated with them.

_Conclusions and Recommendations about Issue 10:_

SPM should specify means to associate multiple ids with the same

resource. It may be that owl:sameAs is adequate, but use cases

should be developed and the semantics of owl:sameAs examined to see

if it satisfies them. This may be in the scope of (Cryer et

al. 2009)

*Issue 11:* It is unclear how the data provider is to explain the

intended meaning behind possibly ambiguous sets of statements. For

example- A taxon name string may be provided twice with different

languages, for example English or Latin. In this case it's to be

understood that the name can be in either Latin or English but

depending on the consuming applications' reasoning -the first may be

taken as the primary, the second as the second. But the generated

RDF would usually be order independent, making it difficult to

track.

_Conclusions and Recommendations about Issue 11:_

SPM should specify mechanisms and practices that allow a provider to

signify relationships among alternatives. rdf:List may not be

adequate if statements appear independently of one another (for

example, after data integration).

*Issue 12:* Lack of Metadata about the served SPM: We found no clear

way to document within the SPM file how the SPM itself was

produced. We resorted to XML comments, but it is unclear whether

some standard RDF annotation mechanism might be better. Of special

importance might be provenance of the SPM, including original

source, changes, versions, etc.

_Conclusions and Recommendations about Issue 12:_

There should be best practices established for annotating service

output, and it should be examined whether SPM has any specific

needs.