With EOL’s transition the new look and site organization, EOL 2.0 as they call it, there was a significant period of time when there were no harvests made, this meaning that I could’t verify the Phenoscape content in the new look.

There was a pleasant surprise when I discovered that the content went public.

For now, all the morphollogy data for the 9 taxa that I offered for harvest is in its rightful place, in the specie’s page. Here’s one of them:

http://eol.org/pages/204762/details#morphology

EOL also offers monthly page views statistics for each content partner. Here are the statistics for november :

Seeing all this encouraged me to add more taxa for harvest and finally to prepare all the data from Phenoscape that is eligible for publishing in EOL.

Having taxa with quite a large text description, it appeared the problem of finding better way to display this information. The regular user will have trouble maintaining focus while  processing a large block of text. There had to be a separation based on a solid principle. After a couple of talks, the idea of grouping the phenotype description by anatomical systems was the winner. Now let’s say if someone was interested in aspects of a species’ skeletal system, this information will quickly pop out.

For the actual grouping, a reasoner over the Teleost Anatomy Ontology was used. Firstly, component classes of each anatomical system were extracted. Having those, for a taxon, intersections between the set of anatomical entities associated with the taxon and sets of anatomical entities representing anatomical systems were done.

The grouping was a success. There remained only the problem of displaying the new text in EOL. Here I said “Keep it simple” and so I did, but this part didn’t go as expected all the way. Surprisingly, the html text didn’t appear in the EOL page identically as in local tests, but fortunately this was just a small arrangement issue.

Here is a screen capture of how the groupings appear.

I will give small samples of two different formatting styles that produced the same result, represented in the above image.

1:

<h2 style="text-align:center;">Skeletal System</h2>
<p>Has a smaller <a href="http://kb.phenoscape.org/term/entity/TAO:0000657">entopterygoid</a>.
Has a <a href="http://kb.phenoscape.org/term/entity/TAO:0001788">pelvic splint</a>.
The <a href="http://kb.phenoscape.org/term/entity/TAO:0001675">mesethmoid cornu</a> is bifurcated.
Presents a larger <a href="http://kb.phenoscape.org/term/entity/TAO:0002025">optic foramen</a>.
</p><h2 style="text-align:center;">Digestive System</h2>
<p>Has a smaller <a href="http://kb.phenoscape.org/term/entity/TAO:0000657">entopterygoid</a>.
Presents a <a href="http://kb.phenoscape.org/term/entity/TAO:0001277">anterior chamber swim bladder</a>. </p>

2:

<p style="text-align:center;"><b><font size="5">Digestive System</font></b></p>
<p>Presents a smaller <a href="http://kb.phenoscape.org/term/entity/TAO:0000657">entopterygoid</a>.
Has a <a href="http://kb.phenoscape.org/term/entity/TAO:0001277">anterior chamber swim bladder</a>. </p>
<p style="text-align:center;"><b><font size="5">Skeletal System</font></b></p>
<p>Presents a smaller <a href="http://kb.phenoscape.org/term/entity/TAO:0000657">entopterygoid</a>.
Presents a <a href="http://kb.phenoscape.org/term/entity/TAO:0001788">pelvic splint</a>.
Has a bifurcated <a href="http://kb.phenoscape.org/term/entity/TAO:0001675">mesethmoid cornu</a>.
Presents a bigger <a href="http://kb.phenoscape.org/term/entity/TAO:0002025">optic foramen</a>. </p>

I managed to link anatomical entities to their definition page on the Phenoscape Knowledgebase  and write them in an export file. This meant that half of the problem was solved. Also, I’ve added a link to the source of the data, the taxon’s page from the Phenoscape Knowledgebase.

Here is a sample of the new export file.

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<response xmlns="http://www.eol.org/transfer/content/0.3" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:dwc="http://rs.tdwg.org/dwc/dwcore/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://services.eol.org/schema/content_0_3.xsd">
	<taxon>
		<dc:identifier>ictalurus_australis</dc:identifier>
		<dwc:ScientificName>Ictalurus australis</dwc:ScientificName>
		<dataObject>
			<dataType>http://purl.org/dc/dcmitype/Text</dataType>
                        <dc:source>http://kb.phenoscape.org/term/taxon/TTO:1045587</dc:source>
			<subject>http://rs.tdwg.org/ontology/voc/SPMInfoItems#Morphology</subject>
			<dc:description xml:lang="en">
Has a bigger <a href="http://kb.phenoscape.org/term/entity/TAO:0002025">optic foramen</a>.
Has a bifurcated <a href="http://kb.phenoscape.org/term/entity/TAO:0001675">mesethmoid cornu</a>.
Presents a larger <a href="http://kb.phenoscape.org/term/entity/TAO:0000196">dorsal hypohyal bone</a>.
The <a href="http://kb.phenoscape.org/term/entity/TAO:0001058">caudal fin</a> is bifurcated.
Has a smaller <a href="http://kb.phenoscape.org/term/entity/TAO:0000657">entopterygoid</a>.
Has a <a href="http://kb.phenoscape.org/term/entity/TAO:0001788">pelvic splint</a>.
Has a <a href="http://kb.phenoscape.org/term/entity/TAO:0001277">anterior chamber swim bladder</a>.
			</dc:description>
		</dataObject>
	</taxon>
</response>

The second  part was to see how this data will present on an EOL page. I was able to find this out after the harvest and I was glad to see it was as expected.

Here is a print from the EOL page preview.

I registered as a content partner for EOL. The description for the Channel Catfish has been harvested and now I can preview it on the specie’s page. It worked great. Upon the administrator’s decision, the newly added information will be publicly available. Until then, I will post here a screen of how it looks. Maybe some html formatting will help for a better presentation, but at this point it’s a relieve that everything went smooth with obtaining this preview.

The following export file was obtained using only the sample patterns presented in the previous post. As a test case, I stuck with the same fish, Channel catfish .

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<response xmlns="http://www.eol.org/transfer/content/0.3" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:dwc="http://rs.tdwg.org/dwc/dwcore/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://services.eol.org/schema/content_0_3.xsd">
	<taxon>
		<dc:identifier>ictalurus_punctatus</dc:identifier>
		<dwc:ScientificName>Ictalurus punctatus</dwc:ScientificName>
		<dataObject>
			<dataType>http://purl.org/dc/dcmitype/Text</dataType>
			<subject>http://rs.tdwg.org/ontology/voc/SPMInfoItems#Morphology</subject>
			<dc:description xml:lang="en">
Presents a coronomeckelian. Has a bigger maxilla. Has an urohyal median process. Has a posterior cranial fontanel.
The caudal fin is bifurcated. Has a posterior dentation of pectoral fin spine. Has a mesocoracoid bone. Has a bigger claustrum bone.
Presents a hypobranchial 2 bone distal cartilage. Presents a gill raker. Presents an interhyal bone. Presents an ossified basibranchial element.
Presents an ossified hypobranchial 2 element. Has a vomer. Presents an epibranchial 5 cartilage. Has a bifurcated mesethmoid cornu.
Presents an ossified mesethmoid bone. Presents a quadrate-hyomandibula joint. Has a smaller ceratobranchial 3 bone distal cartilage. Presents a smaller anterior cartilage of palatine.
Presents a distal cartilage of external anterior process of basipterygium. Presents a posterior limb of parapophysis 4. Has an extrascapula. has an ossified basibranchial 3 element.
Presents a smaller infraorbital 5. Presents an optic foramen. Presents a parapophysis. Has a smaller entopterygoid.
Presents a supraneural 3 cartilage. Has an anterior cranial fontanel. Has an anterior chamber swim bladder. Has a lateral ethmoid wing.
Presents a larger Meckel's cartilage. Presents a larger mesethmoid bone. Has a posterior nasal barbel. Presents a coronoid process.
Presents an internal anterior process of basipterygium. Presents an inner mental barbel. Has a bigger distal cartilage of posterior process of basipterygium. Has an autopalatine-maxillary joint.
Has a lateral ethmoid-ectopterygoid ligament. Presents an adipose fin. Presents a dorsal hypohyal bone. Has a mandibular sensory canal.
Presents a smaller infraorbital 4. Has a mesethmoid cornu. Presents a pelvic splint. Presents a bigger dorsal hypohyal bone.
Presents a smaller maxilla. Presents a pharyngobranchial 1 element. Presents an interopercular-mandibular ligament. Has a superficial ophthalmic nerve foramen.
Presents an external anterior process of basipterygium. Presents an ossified hypobranchial 1 element. Has an urohyal lateral process. Presents a ceratobranchial 5 tooth.
Presents an ossified hypobranchial element. Presents a vomerine tooth. Presents a distal cartilage of internal anterior process of basipterygium. Has a hypobranchial 3 cartilage.
Has an interopercle. Presents a retractor tentaculi. has an ossified pharyngobranchial 4 element. Presents a hypobranchial 2 bone.
Presents a hypobranchial 1 bone. Presents a posterior cleithral process. Presents a hypobranchial element. Presents an outer mental barbel.
Presents a smaller distal cartilage of external anterior process of basipterygium. Presents an anterior limb of parapophysis 4. Presents a bigger optic foramen.
			</dc:description>
		</dataObject>
	</taxon>
</response>

I present below a sample of a XML draft for connecting phenotype quality terms to possible sentences.

Firstly, I want to give the interpretation rules for the pattern tag.
- | = only one token (word or word group) will be randomly chosen from all tokens inclosed in a “()” and that are separated by “|”.
- [indefinite_article] = will be properly generated depending on the first letter of the phenotype entity
- * = any phenotype entity.

As can be seen in the example below, a phenotype quality can be associated with more than one pattern.

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<phenotypeQualities>
   <phenotypeQuality>
      <name>present</name>
      <pattern>(presents|has) [indefinite_article] *</pattern>
   </phenotypeQuality>
   <phenotypeQuality>
      <name>decreased size</name>
      <pattern>(presents|has) a smaller *</pattern>
   </phenotypeQuality>
   <phenotypeQuality>
      <name>increased size</name>
      <pattern>(presents|has) a (bigger|larger) *</pattern>
   </phenotypeQuality>
   <phenotypeQuality>
      <name>bifurcated</name>
      <pattern>(presents|has) a bifurcated *</pattern>
      <pattern>the * is bifurcated</pattern>
   </phenotypeQuality>
   <phenotypeQuality>
      <name>round</name>
      <pattern>(presents|has) a round *</pattern>
   </phenotypeQuality>
   <phenotypeQuality>
      <name>ossified</name>
      <pattern>(presents|has) an ossified *</pattern>
   </phenotypeQuality>
</phenotypeQualities>

I guess I waited so long for a post because I wanted to have something real to show.

The first result I have for Encyclopedia of Life is an export file for the Ictalurus punctatus taxon. It isn’t much, but it could be compared to information already provided by some EoL pages, for example the following Dacus merzi page.

My export file is below:

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<response xmlns="http://www.eol.org/transfer/content/0.3" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:dwc="http://rs.tdwg.org/dwc/dwcore/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://services.eol.org/schema/content_0_3.xsd">
   <taxon>
      <dc:identifier>ictalurus_punctatus</dc:identifier>
      <dwc:ScientificName>Ictalurus punctatus</dwc:ScientificName>
      <dataObject>
         <dataType>http://purl.org/dc/dcmitype/Text</dataType>
         <subject>http://rs.tdwg.org/ontology/voc/SPMInfoItems#Morphology</subject>
         <dc:description xml:lang="en">Presents a coronomeckelian. Presents an urohyal median process. Presents a posterior cranial fontanel. Presents a posterior dentation of pectoral fin spine.
Presents a mesocoracoid bone. Presents a hypobranchial 2 bone distal cartilage. Presents a gill raker. Presents an interhyal bone.
Presents a vomer. Presents an epibranchial 5 cartilage.Presents a quadrate-hyomandibula joint. Presents a distal cartilage of external anterior process of basipterygium.
Presents a posterior limb of parapophysis 4. Presents an extrascapula. Presents an optic foramen. Presents a parapophysis. Presents a supraneural 3 cartilage.
Presents an anterior cranial fontanel. Presents an anterior chamber swim bladder. Presents a lateral ethmoid wing. Presents a posterior nasal barbel. Presents a coronoid process. Presents an internal anterior process of basipterygium. Presents an inner mental barbel.
Presents an autopalatine-maxillary joint. Presents a lateral ethmoid-ectopterygoid ligament. Presents an adipose fin. Presents a dorsal hypohyal bone. Presents a mandibular sensory canal.
Presents a mesethmoid cornu. Presents a pelvic splint. Presents a pharyngobranchial 1 element. Presents an interopercular-mandibular ligament. Presents a superficial ophthalmic nerve foramen. Presents an external anterior process of basipterygium.
Presents an urohyal lateral process. Presents a ceratobranchial 5 tooth. Presents a vomerine tooth. Presents a distal cartilage of internal anterior process of basipterygium. Presents a hypobranchial 3 cartilage. Presents an interopercle.
Presents a retractor tentaculi. Presents a hypobranchial 2 bone. Presents a hypobranchial 1 bone. Presents a posterior cleithral process. Presents a hypobranchial element. Presents an outer mental barbel. Presents an anterior limb of parapophysis 4. </dc:description>
      </dataObject>
   </taxon>
</response>