3-5
March 2003, U.Penn.
Present:
Chris Stoeckert, Trish Whetzel, Helen Parkinson, John Matese, Paul Spellman,
Joe White.
Aims
of POW3:
Completion
of the Core Ontology
Adding
instances
Identifying
contact domains for annotation.
Full
annotation examples, including BioMaterial.
Education
in area of data transformation to get new instances.
Future
POW 4
Possible
date May 10, location TBD.
Invite
special interests to join.
POW5?
possibly in July, to focus on software which implements the ontology.
Completed
annotation examples for discussion.
Interfacing
with external ontologies.
Including
disjoints and other constraints.
MGED6
Tutorials
required, one for MAGE coders, one for biologists. Getting the ontology
validated by MAGE developers was discussed, Angel, Ugis, Mahendra, NCICB,
Genex, Jax, Jason Goncalves @ Iobion, Rosetta all possible candidates. Time
frames were either pre or post MGED 6.
Notes
on POW3
------------
BioSample
and BioSource defs changed to make the differences explicit.
Instances
added to classes:
HardwareType
(not a long list, policy not to include supplies, just major hardware).
FailType
WarningType
ControlType
AtomicAction*
cross check with protocol to ensure completeness
ComplexAction
Instances
from both the Action subclasses were examined to ensure that they were
correctly classified and some were moved after discussion. We also agreed that
we should create as few terms as possible and that these should not overlap if
possible.
Paul
suggested a change_environment instance - when used a biomaterial
characteristic should have changed, the instance was renamed
change_biomaterial_characteristic to reflect this.
ProtocolType
ImageFormat
FeatureShape
SoftwareType
MAGE
concepts addressed:
Transformation,
is in the extended ontology, isn't part of the core as doesn't need an
OntologyEntry, should be addressed after the core ontology is finished.
DatabaseQualityControl,
intended to be descriptive text in MAGE, allowed to have OntologyEntry, created
as such within the ontology as it was decided that this information should be
described by an OntologyEntry for query purposes. Three new classes added,
ReplicateDescripion, NormalizationDescription, QualityControlDescription plus
named type classes to hold the OntologyEntry information. Instances not yet
added to these classes but possible values of the QualityControlDescriptionType
could be dye swap, peer review, array type quality control.
NormalizationDescriptionType instance will require working with the
DataProcessing working group.
ExperimentalFactor:
Examples:
ExperimentalFactor
Problems
with grouping these were addressed. 1. it's not possible in MAGE to group Factors
easily by Bioassay and channel:
10
mm NaCl, 10% glucose
150mm
Nacl, 1% glucose
All
factors can be expressed but only singly and the current MAGE model has an
(un-enforceable) rule that there should be only one factor value per
TopLevelBioAssay. This means that there is no way to express which combination
of factors were applied, or which channel they belong two. This is a serious
problem for two channel experiements.
Paul
suggested that this is a serious problem with the model and should be resolved
within the Ontology if possible. The POW took the decision to create two new
Classes which describe factor value. These will be encoded in MAGE By means of
PropertySets attached to Factor Values. The only one factor value per
TopLevelBioAssay rule will be discarded as it is not enforceable anyway. This
will not affect code and a small test MAGE-ML example was found to be valid.
Paul offered to provide a code example (action item Paul) in addition to the
small one coded by Helen at the meeting.
ExperimentalFactorCategories
In
some of the examples of the experiment package coded by various members of the
group there was a problem describing certain factors. The problem is limited to
those factor values that are a string.
E.g.
If an experiment is a strain comparison the strain names do not belong in
FactorCategory but some descriptor indicating that this is a strain comparison.
We
therefore decided to make a new class to hold these top level terms and classes
within the BioMaterialCharacteristics were used to create these instances. So
that the class name StrainOrLine is also an instance strain_or_line. The class
containing these instances is:
BioMaterialCharacteristicCategory
example instances are strain_or_line, organism_part.It was also noted that we
may not have been working from the most recent PNG's. The most recent and
extensive Documentation prepared by Cathy Ball has some PNG's which need to be
replaced. The most recent PNG's were distributed and Helen offered to update
Cathy's documentation.
A
second task is that the Ontology was constructed on the basis of the previous
documentation and now needs to be checked to ensure all the OntologyEntries are
represented. (*action item Helen).
Databases
and external Ontology entries.
In
the revised MAGE png's there is an association from OntologyEntry via
OntologyReference to DatabaseEntry, this in turm has an assn to DataBase. Helen
proposed that these should be within the ontology, along with URIs and
descriptions so that both databases (like ArrayExpress) and users of the
Ontology can clearly identify databases. This information will be in both the
Ontology and declared in the DescriptionPackge of MAGE and these will therefore
be consistent.
Meeting
with Gilberto Fragoso and LiJu Fan from NCICB.
The
various tools and ontologies from NCICB were introduced. Some of these will be
very useful, e.g., compounds, drugs, cancer anatomy terms. Some NCICB terms are
taken from other known ontologies, e.g., mouse terms from the Jackson Labs. The
ontologies are not in a wholly useable form as they may not have visible unique
id's which are easy for a user to point at and include in their annotation.
NCICB are interested in doing some work to make these id's available.
The
gene expression database at NCI already uses some of the MIAME concepts, LiJun
brought a mapping of the MIAME concepts to NCI own terms concepts. These need
to be modified to reflect changes in MAGE and these were discussed. LiJun now
has the MAGE-MIAME mapping document.
Action
Items:
Code
Factors grouped via PropertySets and applied multiply to TopLevelBioAssays,
Paul
Coding
of a Cancer data set to show to Gilberto and NCICB, Helen
Check
through Ontology for:
typos,
Trish
missing
associations especially of instances, Trish
instances,
properties, classes all defined an all in use, report on those which are not,
Helen
Compile
a list of databases and ontologyentries, update the website with these plus add
appropriate descriptions that poimnt users to multiple vocabularies where they
exist. E.g.TAIR has plant specific GO terms, OrganismPart and
DevelopmentalStage terms. John/Helen
Trish
has raised additional items::
checking
has_type assn to ensure used consistently -Trish
modification
of defintion of "cell"
for MaterialType to be
stated
as "one or more cell excluding single cell organisms".