Building SADI Services Tutorial - SIB Workshop, Geneva, December 2015

Beyond the Triplestore
http://tiny.cc/SADI_Tutorial
Slides, copy/paste code, and example
data are all in this Google folder
All content licensed CC-BY
Mark D. Wilkinson, CBGP-UPM, Madrid
markw@illuminae.com

Contact me anytime!
markw@illuminae.com
I’m the SADI “Helpdesk”
:-)

First:
Why SADI?
Then:
Examples of SADI simple Linked Data
Followed by:
Examples of SADI with “deep semantics”
Finally:
How to build it yourself!

Semantic Web Technologies
?TO ME: If you are using RDF or even OWL, without reasoning, then you
are ‘doing’ Linked Data. When you start using a reasoner (or reasoning of
some type) you are ‘doing’ Semantic Web

?I will be showing how SADI can be used both as a straightforward
Linked Data resource, and/or as a Semantic Web resource.

?Key Message:
You do not have to “get” OWL
to use SADI effectively

The Semantic Web
causally related to

In My Opinion, this is the critical bit!
causally related to
The link is explicitly labeled!
???

http://semanticscience.org/resource/SIO_000243
SIO_000243:
<owl:ObjectProperty rdf:about="&resource;SIO_000243">
<rdfs:label xml: lang="en"> is causally related with</rdfs:label>
<rdf:type rdf:resource="&owl;SymmetricProperty"/>
<rdf:type rdf:resource="&owl;TransitiveProperty"/>
<dc:description xml:lang="en"> A transitive, symmetric, temporal relation
in which one entity is causally related with another non-identical entity.
</dc:description>
<rdfs:subPropertyOf rdf:resource="&resource;SIO_000322"/>
</owl:ObjectProperty>
causally related with

A lot of important information cannot be represented
on the Semantic Web
For example, all of the data that results from
analytical algorithms and statistical analyses

Varying estimates
put the size of the
Deep Web
between
500 and 800 times
larger than the
surface Web

On the WWW
“automation” of
access to Deep Web
data happens through
“Web Services”

There are many suggestions for how to bring the Deep Web
into the Semantic Web using Semantic Web Services (SWS)

Describe input data
Describe output data
Describe how the system manipulates the data
Describe how the world changes as a result

Describe input data
None, so far, has proven to be wildly successful
(in my opinion)

Describe input data
None, so far, has proven to be wildly successful
(in my opinion)
…because describing what a Service does is HARD!

Lord, Phillip, et al. The Semantic Web–ISWC 2004 (2004): 350-364.

Scientific Web Services are DIFFERENT!
They’re simpler!
So perhaps we can solve the Semantic Web Service problem
as it pertains to this (important!) domain

With respect to the Semantic Web
What is missing from this list?
Describe input data

The Semantic Web gets its power from
relationships

Relationships are not on this list…
and that seemed to me to be a huge oversight!
Describe input data

In 2008 I published a set of design-patterns
for scientific Semantic Web Services
that focuses on the biological relationship that the Service “exposes”

AACTCTTCGTAGTG...
BLAST
Web Service

AACTCTTCGTAGTG...
BLAST
sequenceX
has_seq_string

AACTCTTCGTAGTG...
BLAST
has
homology
to
Terminal Flower
type
gene
species
A. thal.
sequenceX
has_seq_string
AACTCTTCGTAGTG...
sequenceX
has_seq_string

AACTCTTCGTAGTG...
BLAST
has
homology
to
Terminal Flower
type
gene
species
A. thal.
SADI requires you to explicitly declare
as part of your analytical output,
the biological relationship between
the input and the output that your
algorithm “exposed”.
sequenceX
has_seq_string
AACTCTTCGTAGTG...
sequenceX
has_seq_string

If SADI produces Linked Data, can we interact with it
like any other Linked Data resource?

“Semantic Health And Research Environment”
SPARQL + SADI + Workflows + OWL Reasoning

The SHARE registry
indexes all of the input/output/relationship
triples that can be generated by all known SADI services
SHARE is then able to discover Services
that will generate the data that it needs
to answer the SPARQL query

What is the phenotype of every allele of the
Antirrhinum majus DEFICIENS gene
SELECT ?allele ?image ?desc
WHERE {
locus:DEF genetics:hasVariant ?allele .
?allele info:visualizedByImage ?image .
?image info:hasDescription ?desc
}

WHERE {
}
Note that there is no “FROM” clause!
We don’t tell it where it should get the information,
The machine has to figure that out by itself...

WHERE {
}
Starting data: the locus “DEF” (Deficiens)
(the “bound” variable in the query)

WHERE {
}
Query: A series of relationships v.v. DEF

...and in a few seconds you get your answer.
Based on the relationships in your query, SHARE queried its registry
to automatically discover SADI Services capable of generating those triples

This is Linked Data, like any other…

What pathways does UniProt protein P47989 belong to?
PREFIX pred: <http://sadiframework.org/ontologies/predicates.owl#>
PREFIX ont: <http://ontology.dumontierlab.com/>
PREFIX uniprot: <http://lsrn.org/UniProt:>
SELECT ?gene ?pathway
WHERE {
uniprot:P47989 pred:isEncodedBy ?gene .
?gene ont:isParticipantIn ?pathway .
}

What pathways does UniProt protein P47989 belong to?
PREFIX pred: <http://sadiframework.org/ontologies/predicates.owl#>
PREFIX ont: <http://ontology.dumontierlab.com/>
PREFIX uniprot: <http://lsrn.org/UniProt:>
SELECT ?gene ?pathway
WHERE {
uniprot:P47989 pred:isEncodedBy ?gene .
?gene ont:isParticipantIn ?pathway .
}
Note again that there is no “From” clause…
I have not told SHARE where to look for the answer, I
am simply asking my question

Two different
providers of gene
information
(KEGG & NCBI);
were found &
accessed
Two different
providers of
pathway
information
(KEGG and
GO);
were found &
accessed

Again, the results are all links to the original data

These were examples where SADI/SHARE was used
for “simple” Linked Data exploration
What does it look like when we start pushing Semantics?
Please be assured - you DO NOT have to understand
this next piece in order to use SADI. This is just
“the icing on the cake”
“c'est la cerise sur le gâteau”
“la guinda del pastel”
“die Krönung des Ganzen”

Show me the latest Blood Urea Nitrogen and Creatinine levels
of patients who appear to be rejecting their transplants
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX patient: <http://sadiframework.org/ontologies/patients.owl#>
PREFIX l: <http://sadiframework.org/ontologies/predicates.owl#>
SELECT ?patient ?bun ?creat
FROM <http://sadiframework.org/ontologies/patients.rdf>
WHERE {
?patient rdf:type patient:LikelyRejecter .
?patient l:latestBUN ?bun .
?patient l:latestCreatinine ?creat .
}

Show me the latest Blood Urea Nitrogen (BUN) and
Creatinine levels of patients who appear to be
rejecting their transplants
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX patient: <http://sadiframework.org/ontologies/patients.owl#>
PREFIX l: <http://sadiframework.org/ontologies/predicates.owl#>
SELECT ?patient ?bun ?creat
FROM <http://sadiframework.org/ontologies/patients.rdf>
WHERE {
?patient rdf:type patient:LikelyRejecter .
?patient l:latestBUN ?bun .
?patient l:latestCreatinine ?creat .
}

Likely Rejecter:
A patient who has creatinine levels
that are increasing over time
- - Mark D Wilkinson’s definition

Likely Rejecter:
…but there is no “likely rejecter”
column or table in our database…
only blood chemistry measurements
at various time-points

Likely Rejecter:
So the data required to answer this question
DOESN’T EXIST!

My definition of a Likely Rejecter is encoded in
a machine-readable document written in the OWL Ontology language
Basically:
“the regression line over creatinine measurements should have an increasing slope”

Our ontology refers to other ontologies (possibly published by other people)
to learn about what the properties of “regression models” are
e.g. that regression models have slopes and intercepts
and that slopes and intercepts have decimal values

Based on the Class definition
SHARE decides that it needs to do a
Linear Regression analysis
on the blood creatinine measurements

The conversation between SHARE and the registry
reveals the use of “Deep Semantics”
Q: Is there a SADI service that will consume instances of Patient and give
me instances of LikelyRejector
A: No
Q: Okay... LikelyRejectors need a regression model of increasing slope
over their BloodCreatinine, so... Is there a SADI service that will consume
BloodCreatinine over time and give me its linear regression model?
A: No
Q: Okay... Blood Creatinine over time is a subclass of data of type
X/Y coordinate, so is there a service that consumes X/Y data and
returns its regression model?
A: Yes → here’s the Service URL.

The SHARE system utilizes DL Reasoning over SADI interface
definitions to discover analytical services
that do linear regression analysis
→ sends the data to be analyzed

This happens iteratively
(e.g. SHARE also has to examine the slope of the regression line
using another service, find the “latest” in a series of time measurements, etc.)
There is reasoning after every Service invocation
(i.e. after every clause in the query)
Once it is able to find instances (OWL Individuals)
of the LikelyRejector class, it continues with the
rest of the query

The way SHARE “interprets” data varies
depending on the context of the query
(i.e. which ontologies it reads – Mine? Yours?)
and on what part of the query
it is trying to answer at any given moment
(which ontological concept is relevant to that clause)

Example?
Blood Creatinine measurements
were not dictated to be
Blood Creatinine measurements

Example?
The data had the ‘qualities/properties’ that
allowed one machine to interpret
that they were Blood Creatinine measurements
(e.g. to determine which patients were rejecting)

Example?
But the data also had the ‘qualities/properties’ that
allowed another machine to interpret them as
Simple X/Y coordinate data
(e.g. the Linear Regression calculation tool)

Benefit
of Deep Semantics
Data is amenable to
constant re-interpretation

http://www.flickr.com/people/faernworks/

We will examine SADI
mainly as a source of Linked Data
We will not spend much time
thinking about the Semantics
of our services or their interfaces

2 Contents
1. Introduction to Semantic Web Services
2. Introduction to SADI services
3. SADI service ontologies
4. SADI service generator
5. SADI and SAWSDL
6. SADI clients

2.1.3 Motivation for SADI
▪▪ simple
“perfection is finally attained not when there is no
longer anything to add, but when there is no longer
anything to take away”
▪▪ powerful
“everything should be as simple as it can be, but not
simpler”
▪▪ flexible
“SADI: there’s nothing to it”

2.2 Introduction to SADI Services
2. Introduction to SADI Services
1. What is a SADI service?
2. Why use SADI services?
3. Requirements for SADI compliance
4. Calling a SADI service
5. Advanced SADI features
6. The SADI registry

2.2.1 What is a SADI service?
● SADI services
○ use simple HTTP operations
■ (no project-specific protocol)
○ consume and produce RDF data
■ (no project-specific message scaffolding)
○ use OWL to describe service interface
(use existing ontologies
and especially existing properties)

● input is an RDF graph
○ rooted at a particular node
○ described by an OWL class
● output is an RDF graph
○ rooted at the same node
○ described by another OWL class

● explicit relationship between input and output
○ transparent service operation semantics
● machine-understandable description of the
service interface
○ easy service discovery and integration

2.2.2 Why use SADI services?
Input
height weight
SADI
Service
Output
BMI
ID Name Height Weight Age
24601
7474505B
6
Jean Valjean
Jake Blues
—
...
1.8m
1.73m
1.88m
...
84kg
101kg
75kg
...
45
31
39
...
Client
BMI

Input
height weight
SADI
Service
Output
BMI
24601
7474505B
6
Jean Valjean
Jake Blues
—
...
1.8m
1.73m
1.88m
...
84kg
101kg
75kg
...
45
31
39
...
Client
BMI
#24601
1.8m 84kg
height weight

Input
height weight
SADI
Service
Output
BMI
24601
7474505B
6
Jean Valjean
Jake Blues
—
...
1.8m
1.73m
1.88m
...
84kg
101kg
75kg
...
45
31
39
...
Client
BMI
#24601
25.9
BMI
25.9

@prefix rdf:
@prefix rdfs:
@prefix xsd:
@prefix mged:
@prefix foaf:
<http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
<http://www.w3.org/2000/01/rdf-schema#> .
<http://www.w3.org/2001/XMLSchema#> .
<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#> .
<http://xmlns.com/foaf/0.1/> .
<http://sadiframework.org/examples/bmi-input.rdf#patient24601> bmi:BMI
"25.9"^^xsd:double ;
foaf:name "Jean Valjean"^^xsd:string ; mged:has_height
[ a mged:Measurement ; mged:has_units mged:m ; mged:
has_value "1.8"^^xsd:double
] ;
mged:has_mass
[ a mged:Measurement ;
mged:has_units mged:kg ; mged:
has_value "84"^^xsd:double
] .
Client
24601
1.8m 84kg
height weight
BMI
25.9

sadi: <http://sadiframework.org/ontologies/predicates.owl#> sadi: <http:
//sadiframework.org/ontologies/predicates.owl#> dumontier:
<http://ontology.dumontierlab.com/>
kegg: <http://lsrn.org/KEGG_PATHWAY:>
?gene ?protein ?seq
PREFIX
PREFIX
PREFIX
SELECT
WHERE {
kegg:hsa00232 dumontier:hasParticipant ?gene .
?gene sadi:encodes ?protein .
?protein sadi:hasSequence ?seq
}
Service
Service
Servic
e
Similar to “Federated Queries”… but are actually Web Service Workflows

2.2.3 Requirements for SADI compliance
● Identified by an HTTP URL
○ used to identify the service
■ (service URI)
○ used to invoke the service
■ (service URL)
http://sadiframework.org/examples/hello

•Responds to HTTP GET with service interface def.
•RDF document
•Service definition instance identified by service URI
•(see §2.3.1 for specifics)
•Indicates input OWL class and output OWL class
• (among other things)

input OWL class is
http://sadiframework.org/examples/hello.owl#NamedIndividual
output OWL class is
http://sadiframework.org/examples/hello.owl#GreetedIndividual

● Responds to HTTP POST by invoking service
○ input is an RDF document
■ contains input OWL class instances
○ output is an RDF document
■ contains output OWL class instances
● one for each input instance
● Input/output instance share same URI

input:
@prefix hello: <http://sadiframework.org/examples/hello.owl#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
<http://sadiframework.org/examples/hello-input.rdf#1> a hello:NamedIndividual ;
foaf:name "Guy Incognito" .
output:
<http://sadiframework.org/examples/hello-input.rdf#1> a hello:GreetedIndividual ;
hello:greeting "Hello, Guy Incognito!" .

● Indicates error with appropriate HTTP status
○ usually 500 Internal Service Error
○ may return RDF describing the error

2.2.4 Calling a SADI service
1. Client sends POST request to service URL
● POST body is an RDF document
○ contains input OWL class instances
○ input serialization specified in
Content-type HTTP header
application/rdf+xml text/rdf+n3
○ output serialization requested in
Accept HTTP header

POST /examples/hello HTTP/1.1 Host: sadiframework.org Content-type:
text/rdf+n3 Accept: text/rdf+n3

Note that there is NO special message structure! This is not like SOAP!

2. Service responds with output
● response body is an RDF document
○ contains output OWL class instances
● serialization specified in
○ Content-type HTTP header

HTTP/1.1 200 OK
Content-type: text/rdf+n3

2.2.5 Advanced SADI features
5. Advanced SADI features
a. Asynchronous SADI services
b. Parameterized SADI services

2.2.5.a Asynchronous SADI services
● Problem
○ HTTP timeout if a service takes too long to
respond
● Solution
○ service returns stub immediately; client polls
for complete response

1. Client sends POST request to service URL
● POST body is an RDF document
○ contains input OWL class instances
● input serialization specified in
● output serialization requested in
Accept HTTP header
(Exactly the same as before….)

2. Service responds with stub
● HTTP response code is:
202 Accepted but incomplete
contains output OWL class instances composed of rdfs:
isDefinedBy statements
● serialization specified in:
application/rdf+xml, text/rdf+n3, etc

HTTP/1.1 202 Accepted Content-type: text/rdf+n3
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
rdfs:isDefinedBy <http://sadiframework.org/examples/hello?poll=1> .

3. Client fetches asynchronous data
● fetch the object URL of each
rdfs:isDefinedBy statement
GET /examples/hello?poll=1 HTTP/1.1 Host: sadiframework.org

4. Until output is ready
● service sends an HTTP 302 redirect
Retry-after HTTP header suggests how long the client
should wait (in seconds)
HTTP/1.1 302 Moved Temporarily Retry-After: 30
Location: http://sadiframework.org/examples/hello?poll=1

5. Client follows redirect
● after waiting as suggested by
Retry-after HTTP header
GET /examples/hello?poll=1 HTTP/1.1 Host: sadiframework.org

6. When output is ready
should be combined with original response
HTTP/1.1 200 OK
Content-type: text/rdf+n3

2.2.6 The SADI registry
● clients need to find SADI services
○ ideally just search the Web for instances of the
SADI service description class
■ current technology isn’t quite there
● use the SADI registry
○ SPARQL endpoint, Java and REST APIs
○ anyone can register a service
○ services are indexed by the properties they
attach

2.2.6 The SADI registry
SADI registry
http://sadiframework.org/registry/
SPARQL endpoint
http://sadiframework.org/registry/sparql
REST API
http://sadiframework.org/registry/api/

2.3.2 Input and output OWL classes
2. Input and output OWL classes
a. Input OWL classes
b. Output OWL classes

Remember the OWL2 presentation yesterday
by Frédéric Bestian…
The dangers of OWL reasoning!

Human equivalent to (leg minimum cardinality 2)
→ you not human if you lose a leg

Do SADI Services suffer this problem?

NO!
We are not trying to “understand” the world!

NO!
We are only trying to discover acceptable input

If my analysis requires that you have 2 legs
and you have only one leg...
YOU ARE NOT A CANDIDATE
FOR MY ANALYSIS. PERIOD.

If my analysis requires that you have 2 legs
and you have only one leg...
...my service isn’t interested in whether or not
you are human… it only wants your legs!

2.4.1 Exercise
Create a SADI service that takes
height and weight as input
and attaches BMI.

SADI Services in Perl
The Perl module in CPAN is:
SADI::Simple
Example Service Code:
https://docs.google.com/document/d/1HrFNxG2-eZhiaCaBjNLcAtHPY_-MLCw9BwFmnw4BHKQ/edit?usp=sharing
Example Data and other information:
https://docs.google.com/document/d/1DdWux6w3RzMGexFHf9roRuJnCiDaxWJScECK4POg6RQ/edit?usp=sharing

Building SADI Services Tutorial - SIB Workshop, Geneva, December 2015

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