Obsolete ENVO classes retrieved about ontobee HOT 6 CLOSED

I recommend doing something like ontobee, e.g. rendering with strikethrough

from ontobee.

I would suggest not filtering by default but instead a) show a clearly visible visual indicator with the term(eg strike through and badge on page) and b) have any obsolete terms sorted to the end of results. Perhaps have a cookie-remembered checkbox asking for them not to be shown, not checked by default.

The principle is to ensure that the principle that terms don't just disappear I reinforced. In addition obsolete terms may have useful information such as deprecation reason or suggested alternatives.

The suggested checkbox is for people who are familiar enough that they understand what they will be missing. Remember the state by cookie is to avoid irritating users that choose this option.

from ontobee.

There are several issues related to Pier’s ENVO example:

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ENVO_00002993">

<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tropical humid forests</rdfs:label>

<oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ENVO</oboInOwl:hasOBONamespace>

<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ENVO:00002993</oboInOwl:id>

<oboInOwl:consider rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ENVO:01000228</oboInOwl:consider>

<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>

/owl:Class

Here the classification of the term as deprecated is different from classifying it as a subclass of an “obsolete” class. It provides an Boolean value. Ontobee has not handled this issue yet.

Another issue is how to clearly show it’s an obsolete or deprecated class, such as using the strikethrough sign.

I have discussed with Edison. He will be working on it soon. Once an outcome is available, we will inform it and ask for feedback.

Oliver

From: Alan Ruttenberg [mailto:[email protected]]
Sent: Tuesday, August 04, 2015 5:11 PM
To: ontoden/ontobee
Subject: Re: [ontobee] Obsolete ENVO classes retrieved (#43)

I would suggest not filtering by default but instead a) show a clearly visible visual indicator with the term(eg strike through and badge on page) and b) have any obsolete terms sorted to the end of results. Perhaps have a cookie-remembered checkbox asking for them not to be shown, not checked by default.

The principle is to ensure that the principle that terms don't just disappear I reinforced. In addition obsolete terms may have useful information such as deprecation reason or suggested alternatives.

The suggested checkbox is for people who are familiar enough that they understand what they will be missing. Remember the state by cookie is to avoid irritating users that choose this option.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/43#issuecomment-127762942.

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from ontobee.

owl:deprecated is standard

On 4 Aug 2015, at 14:35, ontoden wrote:

There are several issues related to Pier’s ENVO example:

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ENVO_00002993">

<rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tropical humid
forests/rdfs:label

<oboInOwl:hasOBONamespace
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ENVO/oboInOwl:hasOBONamespace

<oboInOwl:id
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ENVO:00002993/oboInOwl:id

<oboInOwl:consider
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ENVO:01000228/oboInOwl:consider

<owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true/owl:deprecated

/owl:Class

Here the classification of the term as deprecated is different from
classifying it as a subclass of an “obsolete” class. It provides
an Boolean value. Ontobee has not handled this issue yet.

Another issue is how to clearly show it’s an obsolete or deprecated
class, such as using the strikethrough sign.

I have discussed with Edison. He will be working on it soon. Once an
outcome is available, we will inform it and ask for feedback.

Oliver

From: Alan Ruttenberg [mailto:[email protected]]
Sent: Tuesday, August 04, 2015 5:11 PM
To: ontoden/ontobee
Subject: Re: [ontobee] Obsolete ENVO classes retrieved (#43)

I would suggest not filtering by default but instead a) show a clearly
visible visual indicator with the term(eg strike through and badge on
page) and b) have any obsolete terms sorted to the end of results.
Perhaps have a cookie-remembered checkbox asking for them not to be
shown, not checked by default.

The principle is to ensure that the principle that terms don't just
disappear I reinforced. In addition obsolete terms may have useful
information such as deprecation reason or suggested alternatives.

The suggested checkbox is for people who are familiar enough that they
understand what they will be missing. Remember the state by cookie is
to avoid irritating users that choose this option.

—
Reply to this email directly or view it on
GitHubhttps://github.com//issues/43#issuecomment-127762942.

---

Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues

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Reply to this email directly or view it on GitHub:
#43 (comment)

from ontobee.

Could the obsolete classes also be pushed to the bottom of the list when
doing a general search?

On Tue, Aug 4, 2015 at 11:10 PM, Chris Mungall [email protected]
wrote:

owl:deprecated is standard

On 4 Aug 2015, at 14:35, ontoden wrote:

There are several issues related to Pier’s ENVO example:

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ENVO_00002993">

<rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tropical humid
forests/rdfs:label

<oboInOwl:hasOBONamespace
rdf:datatype="http://www.w3.org/2001/XMLSchema#string
">ENVO/oboInOwl:hasOBONamespace

<oboInOwl:id
rdf:datatype="http://www.w3.org/2001/XMLSchema#string
">ENVO:00002993/oboInOwl:id

<oboInOwl:consider
rdf:datatype="http://www.w3.org/2001/XMLSchema#string
">ENVO:01000228/oboInOwl:consider

<owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean
">true/owl:deprecated

/owl:Class

Here the classification of the term as deprecated is different from
classifying it as a subclass of an “obsolete” class. It provides
an Boolean value. Ontobee has not handled this issue yet.

Another issue is how to clearly show it’s an obsolete or deprecated
class, such as using the strikethrough sign.

I have discussed with Edison. He will be working on it soon. Once an
outcome is available, we will inform it and ask for feedback.

Oliver

From: Alan Ruttenberg [mailto:[email protected]]
Sent: Tuesday, August 04, 2015 5:11 PM
To: ontoden/ontobee
Subject: Re: [ontobee] Obsolete ENVO classes retrieved (#43)

I would suggest not filtering by default but instead a) show a clearly
visible visual indicator with the term(eg strike through and badge on
page) and b) have any obsolete terms sorted to the end of results.
Perhaps have a cookie-remembered checkbox asking for them not to be
shown, not checked by default.

The principle is to ensure that the principle that terms don't just
disappear I reinforced. In addition obsolete terms may have useful
information such as deprecation reason or suggested alternatives.

The suggested checkbox is for people who are familiar enough that they
understand what they will be missing. Remember the state by cookie is
to avoid irritating users that choose this option.

—
Reply to this email directly or view it on
GitHub<
https://github.com/ontoden/ontobee/issues/43#issuecomment-127762942>.

---

Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues

---

Reply to this email directly or view it on GitHub:
#43 (comment)

—
Reply to this email directly or view it on GitHub
#43 (comment).

from ontobee.

OK. Edison just finished another update. The new update works as shown below:

For example, if we search for “forest” in the Ontobee general search (shown on the cover page), we get:
http://www.ontobee.org/browser/search.php?ontology=ENVO&keywords=forest&Submit2=Search+terms

The deprecated (or obsolete) terms are listed at the bottom of the page like this:
[cid:[email protected]]

If we click on the “Show Deprecated Terms”, we can see:
[cid:[email protected]]

Here all the deprecated terms are crossed with a strikethrough line.

We can click on one deprecated term IRI:
http://www.ontobee.org/browser/rdf.php?o=ENVO&iri=http://purl.obolibrary.org/obo/ENVO_00000875
It also shows the term is deprecated in the annotation section:
[cid:[email protected]]

Please check them out and let us know if you have more comments and suggestions.

Thanks!

Edison and Oliver

From: Melanie Courtot [mailto:[email protected]]
Sent: Wednesday, August 05, 2015 5:41 AM
To: ontoden/ontobee
Cc: ontoden
Subject: Re: [ontobee] Obsolete ENVO classes retrieved (#43)

Could the obsolete classes also be pushed to the bottom of the list when
doing a general search?

On Tue, Aug 4, 2015 at 11:10 PM, Chris Mungall <[email protected]mailto:[email protected]>
wrote:

owl:deprecated is standard

On 4 Aug 2015, at 14:35, ontoden wrote:

There are several issues related to Pier’s ENVO example:

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ENVO_00002993">

<rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tropical humid
forests/rdfs:label

<oboInOwl:hasOBONamespace
rdf:datatype="http://www.w3.org/2001/XMLSchema#string
<http://www.w3.org/2001/XMLSchema#string�>> ">ENVO/oboInOwl:hasOBONamespace

<oboInOwl:id
rdf:datatype="http://www.w3.org/2001/XMLSchema#string
<http://www.w3.org/2001/XMLSchema#string�>> ">ENVO:00002993/oboInOwl:id

<oboInOwl:consider
rdf:datatype="http://www.w3.org/2001/XMLSchema#string
<http://www.w3.org/2001/XMLSchema#string�>> ">ENVO:01000228/oboInOwl:consider

<owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean
<http://www.w3.org/2001/XMLSchema#boolean�>> ">true/owl:deprecated

/owl:Class

Here the classification of the term as deprecated is different from
classifying it as a subclass of an “obsolete” class. It provides
an Boolean value. Ontobee has not handled this issue yet.

Another issue is how to clearly show it’s an obsolete or deprecated
class, such as using the strikethrough sign.

I have discussed with Edison. He will be working on it soon. Once an
outcome is available, we will inform it and ask for feedback.

Oliver

From: Alan Ruttenberg [mailto:[email protected]]
Sent: Tuesday, August 04, 2015 5:11 PM
To: ontoden/ontobee
Subject: Re: [ontobee] Obsolete ENVO classes retrieved (#43)

I would suggest not filtering by default but instead a) show a clearly
visible visual indicator with the term(eg strike through and badge on
page) and b) have any obsolete terms sorted to the end of results.
Perhaps have a cookie-remembered checkbox asking for them not to be
shown, not checked by default.

The principle is to ensure that the principle that terms don't just
disappear I reinforced. In addition obsolete terms may have useful
information such as deprecation reason or suggested alternatives.

The suggested checkbox is for people who are familiar enough that they
understand what they will be missing. Remember the state by cookie is
to avoid irritating users that choose this option.

—
Reply to this email directly or view it on
GitHub<
https://github.com/ontoden/ontobee/issues/43#issuecomment-127762942>.

---

Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues

---

Reply to this email directly or view it on GitHub:
#43 (comment)

—
Reply to this email directly or view it on GitHub
#43 (comment).

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/43#issuecomment-127935763.

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

from ontobee.