CONTACTS 

SUBJECTS
Tending Garden of Knowledge
Organic Structure Knowledge Data - Wisdom
Subject Indexing, General
Ontologos, 000602
Ontology Definition
Industry Doesn't Know How to Design KM
Core Enterprise Knowledge Management Chronology SDS Intelligence
AI Has Not Succeeded in Augmenting Daily Work
Ontology
Digging Ditch Organize Complexity Ontology

2012 -    ..
2013 - Summary/Objective
2014 -
201401 - Follow up ref SDS 64 0000, ref SDS 63 0000.
201402 -
201403 - Jack notifies the DKR project that Ontologos can be implemented, but
201404 - provides no evidence nor explanations of what this would entail and
201405 - what benefits would result.  He cites another web site that reviews
201406 - Ontologos and other ontology efforts, giving it good marks, but the
201407 - review is entirely theoretical.  No work product is shown, nor
201408 - described, no time studies are given on how long it takes to create
201409 - and use an ontology, and no examples of use are given. ref SDS 0 0775
201410 - A single experiment is cited as illustrating an ontology, but such
201411 - illustration is not evident at the referenced location.  The site
201412 - provides an alphabetical list of diseases, and is well layed out. This
201413 - may suggest that ontology is either both alphabetizing and/or a design
201414 - function.
201415 - ..
201416 - Submitted ref DIT 1 0001 to Jack responding to his letter, and
201417 - linked to this letter; request additional information on implementing
201418 - ontology and Ontologos.
201419 -
201420 - Submitted ref DIT 2 0001 to GeneClinics, per below, ref SDS 0 4964,
201421 - asking for help in locating application of ontology.
201422 -
201423 -       [On 000607 received letter confirming that the citation is a
201424 -       mistake, and advising there is no information available that
201425 -       supports results reported and conclusions. ref SDS 65 0001
201426 - ..
201427 - Submitted ref DIT 3 0001 to Robert Kent at Ontologos responding
201428 - to his letter offering to comment further, ref DRP 2 0001, received
201429 - yesterday. ref SDS 64 0001
201430 -
201431 -
201432 -  ..
201433 - Digging Ditch Illustrates Complexity That Requires Organization
201434 -
201435 - Requested explanation of how Ontologos would organize task of digging
201436 - a ditch. ref DIT 3 3250
201437 -
201438 - Linked to problem of trip to Mars, reported on 991001. ref SDS 10 0001
201439 -
201440 -    [On 000922 cited reference to digging a ditch. ref SDS 66 KY7F
201441 -
201442 -
201443 -
2015 -
2016 -
2017 - Progress
2018 -
201801 -  ..
201802 - Jack Provides Additional Reference on Practical Use of Ontologoy
201803 -
201804 - Received ref DRT 1 0001 from Jack Park commenting on the letter,
201805 - ref DIP 2 0001 sent yesterday, to Jack and the DKR team, submitting
201806 - Robert Kent's letter on progress with Ontologos, and explaining that
201807 - only SDS can really accomplish KM.
201808 -
201809 - Jack advises he is leaving today for a trip to Paris where he will
201810 - attend a conference on XML.
201811 -
201812 - He says Ontologos is the web site for Robert Kent's representation
201813 - language called OML/CKML, ref DRT 1 1876, and advises that there is
201814 - another web site where OML/CKML has been compared to other ontology
201815 - environments:
201816 -          ..
201817 -          Ontology Exchange Languages for Bioinformatics
201818 -
201819 -
201820 - ...located at...
201821 -
201822 -
201823 -         ttp://www.oasis-open.org/cover/OntologyExchange.html 201824 -
201825 -
201826 - Jack does not indicate where in the reference material this comparison
201827 - occurs.
201828 -
201829 -     Below, the paper found that OML, which is part of Ontologos work
201830 -     product, scored well on a review of capabilities for an ontology.
201831 -     ref SDS 0 2632
201832 -     ..
201833 -     However, the score is entirely theoretical.
201834 -
201835 -     The analysis does not show work product illustrating the form,
201836 -     application, time and cost of the system, nor how it is used and
201837 -     time saved relative to current practice. ref SDS 0 0775
201838 -
201839 -     The one example provided suggests ontology might be another word
201840 -     for design, or it simply means alphabetizing. ref SDS 0 4964
201841 -
201842 -
201843 -
201844 -  ..
201845 - SDS Core Engine of Knowledge Not Reviewed by Jack
201846 -
201847 - Jack does not address the substance of the letter explaining how to
201848 - accomplish KM.
201849 -
201850 -
201851 -
201852 -  ..
201853 - Ontologos Implementation Not Established
201854 -
201855 - Jack reports that if people thoroughly explore Ontologos web site, you
201856 - eventually can download enough information to implement it.
201857 - ref DRT 1 3036
201858 -
201859 - Jack does not give an example of anything he downloaded, where he got
201860 - it nor what he created that implements Ontologos, to support his
201861 - report today.
201862 -
201863 -
2019 -
2020 -
2021 - 1223 called Jack
2022 -   ..
202201 - Wished him bon voyage on his trip.  He will return in two weeks.
202202 -
202203 - Asked if he is aware of any examples or explanations about using
202204 - Ontologos methods, as he cites in his letter today.
202205 -
202206 - Jack said he saw some things on a prior web site, but cannot recall
202207 - what it was, only that it showed Ontologos is useful.
202208 -
202216 - ..
202217 - We reviewed Jack's letter on 000426 explaining SDS on the
202218 - Interent demonstrates proof of concept for a DKR, ref SDS 36 3315, and
202219 - subsequent report on 000503 citing advantages of "Knowledge Space"
202220 - provided by SDS, ref SDS 42 6138,
202221 -
202222 - I asked Jack if he can point to comparable evidence showing proof of
202223 - concept provided by Ontologos?
202224 -
202225 - Jack said he has to leave on his trip.  He does not recall right now,
202226 - but feels sure Robert Kent has implemented Ontologos in some way or
202227 - other.
202228 -
202229 -
202230 -
2023 -

SUBJECTS
Ontology Definition
Ontology Organization Process Subjects Topics Catagories Classficatio
DNA Organic Structure Power Increased by Controlling Microcosm
Organic Structures Greater Control Microcosm of Details Improves Prod

2607 -
260701 -  ..
260702 - Ontology Defined But Implementation Not Established Nor Explained
260703 -
260704 - Follow up ref SDS 17 2622.
260705 -
2608 -
2609 - 1513 reviewed paper
2610 -
261001 - Examined the paper Jack submitted for further explanation of
261002 - Ontologos tools and methods. ref DRT 1 0002
261003 -
261004 -
261005 -            Ontology Exchange Languages for Bioinformatics
261006 -
261007 -
261008 -         ttp://www.oasis-open.org/cover/OntologyExchange.html 261009 - ..
261010 - This source supplements the definition of ontology reviewed on
261011 - 000221. ref SDS 17 6W6N
261012 -
261013 - Ontology means...
261014 -
261015 -
261016 -      ...specifications of the concepts in a given field and the
261017 -      relationships among those concepts. ref DRT 1 4830
261018 -
261019 - ...definition varies according to different authorities...
261020 -
261021 -      ...a specification of a set of concepts, relations, objects, and
261022 -      constraints that define some domain of interest, for reuse across
261023 -      multiple applications. ref DRT 1 7344
261024 -
261025 -          [On 001130 Jack proposes ontology "engine" to improve SDS by
261026 -          automating links and subjects. ref SDS 67 GK8O
261027 -
261028 -          [On 001214 Jack proposes use cases to develop ontology based
261029 -          on Qualitative Process Theory (QPT). ref SDS 68 0001
261030 -
261031 -      a.  controlled vocabulary -- is an ontology that simply lists a
261032 -          set of terms. ref DRT 1 5244
261033 -
261034 -      b.  taxonomy -- is a set of terms that are arranged into a
261035 -          generalization-specialization hierarchy.  A taxonomy does not
261036 -          define attributes of these terms, nor does it define
261037 -          relationships between the terms. ref DRT 1 9200
261038 -
261039 -      c.  object-oriented database schema defines a hierarchy of
261040 -          classes, and attributes and relationships of those classes.
261041 -          ref DRT 1 2688
261042 -          ..
261043 -      d.  knowledge-representation system based on first-order
261044 -          logic can express all of the preceding relationships, as well
261045 -          as negation and disjunction. ref DRT 1 3479
261046 -
261047 -             This supports Eric's new specs received on 000602 that has
261048 -             a section "Relational", ref SDS 61 4967, but there is no
261049 -             evidence showing this can be done, how, and time saved.
261050 -      ..
261051 -      Ontologies are used to develop shared understanding of
261052 -      concepts in a field. ref DRT 1 5016
261053 -      ..
261054 -      Ontologies are used to manage a "data base." ...every
261055 -      biological database employs an ontology, either implicitly or
261056 -      explicitly, to model its data.  The more fine-grained the
261057 -      ontology, the more precisely the database will be able to model
261058 -      the nuances of the data that it tries to capture.  A
261059 -      coarse-grained ontology will model only superficial aspects of
261060 -      the data, and therefore may not capture data elements that are
261061 -      important for some problem-solving task. ref DRT 1 6734
261062 -
261063 -      For example, a genome-sequence database that fails to record
261064 -      which genetic code is used to encode a given DNA sequence does
261065 -      not provide the information that users of the database will need
261066 -      to reliably translate each DNA sequence into the corresponding
261067 -      protein sequence. ref DRT 1 1705
261068 -          ..
261069 -          This explanation reflects the limitations of data base
261070 -          management set out in the record on 000517. ref SDS 53 3976
261071 -
261072 -          This suggests that ontology is too narrow for knowledge
261073 -          management, since it is geared for data base work.
261074 -
261075 -          On 910221 SDS grows organic subject structures like DNA grows
261076 -          living organizms. ref SDS 3 RR5I
261077 -
261078 -
261079 -       ..
261080 -      Semantically Malformed Ontology Corrupts, Restircts Information
261081 -
261082 -      A semantically malformed ontology is one that incorrectly models
261083 -      the semantics of its application domain, and therefore yields a
261084 -      database whose structure corrupts or restricts the information
261085 -      that it is intended to hold. For example, a metabolic database
261086 -      that defines a one-to-one relationships between enzymes and the
261087 -      reactions they catalyze cannot reliably model the fact that a
261088 -      bifunctional enzyme catalyzes two separate reactions. ref DRT 1
261089 -      4056
261090 -
261091 -
261092 -   This is awfully close to saying that ontology is a custom of using
261093 -   the same words and patterns to explain things, which is the essence
261094 -   of culture.
261095 -                               ..
261096 -   We actually need a broader concept for knowledge management,
261097 -   one that builds bridges between fields, not circles around them.
261098 -
261099 -   The challenge of knowledge managment is that it synthesizes ideas
261100 -   and methods from different disciplines, and right now that is hard
261101 -   for people in law, engineering, cognitive science, computer science,
261102 -   philosophy, ship building, construction and so on to accomplish,
261103 -   because they are only talking to themselves.
261104 -
261105 - The paper seeks to standardize an ontology for molecular-biology for
261106 - sharing within the bioinformatics community. ref DRT 1 1760
261107 -
261108 -      The paper defined a set of capabilities that the ideal
261109 -      ontology-exchange language should satisfy.  The study scored the
261110 -      languages according to the degree to which they provided each
261111 -      capability. ref DRT 1 4615
261112 -
261113 -
261114 -  ..
261115 - Ontologos System Reviewed for Application to Bioinfomatics
261116 -
261117 -      Authors performed several ontology-exchange experiments with the
261118 -      two languages that received the highest scores: OML and
261119 -      Ontolingua. ref DRT 1 3068
261120 -
261121 -      The result of those experiments, and the main conclusions of this
261122 -      study, was that the frame-based semantic model of Ontolingua is
261123 -      preferable to the conceptual graph model of OML, but that the
261124 -      XML-based syntax of OML is preferable to the Lisp-based syntax of
261125 -      Ontolingua. ref DRT 1 6150
261126 -
261127 - This sounds like people, who are looking for something useful to do
261128 - with ontologies, described criteria and then evaulated Ontologos and
261129 - Ontolinguia, and found that each has strengths and weaknesses.
261130 - ..
261131 - This does not establish that either can be used in a practical
261132 - way day to day.
261133 -
261134 -
261135 -  ..
261136 - Experiment GeneClinics Suggests Ontology to Organize Web Site
261137 - Ontology Not Illustrated by GeneClinics Web Site
261138 -
261139 - The GeneClinics experiment...
261140 -
261141 -
261142 -                    http://www.geneclinics.org/
261143 -
261144 -
261145 - ...illustrates complexity of different ontologies. ref DRT 1 1156
261146 -
261147 - Review of the web site shows it does not expressly identify anything
261148 - as an "ontology," nor identify anything that leads to a conclusion it
261149 - is using an "ontology."
261150 -     ..
261151 -     Submitted ref DIT 2 0001 to GeneClinics asking for help in
261152 -     locating application of ontology.
261153 -
261154 -       [On 000607 received letter confirming that the citation is a
261155 -       mistake, and advising there is no information available that
261156 -       supports results reported and conclusions. ref SDS 65 0001
261157 -
261158 - This web site lists diseases alphabetically, and provides links to an
261159 - explanation and related information on diagnosis, treatment etc.
261160 -
261161 -     It is not clear from this site that diseases are listed in
261162 -     alternate ways, and by alternate routes.
261163 -
261164 - The web site seems at first impression to be well designed by
261165 - organizing various elements in a manner that is easy to grasp.  It
261166 - does not overwhelm span of attention by providing too much stuff, that
261167 - causes things to be overlooked.
261168 - ..
261169 - Clicking on links to a particular disease opns a web page that
261170 - is again well designed.
261171 -
261172 - One might conclude that "ontology" people are referred to the web site
261173 - for an example of a well organized web site. If so, we already have a
261174 - term for this function... "design," "layout," and "architecture."
261175 -
261176 - If the alphabetical listing of diseases is the ontology, then we have
261177 - a good name for that... alphabetize, order, arrange.
261178 -
261179 - This is not to diminish the possibility that ontology might add an
261180 - important set of new requirements for organizing information, however,
261181 - this web site does not immediately disclose what it might be relative
261182 - to current practice.
261183 -
261184 -
261185 -
261186 -  ..
261187 - No Work Product Provided, No Productivity Improvements Recorded
261188 -
261189 - The paper goes on to describe several experiments, analysis,
261190 - evaluation and recommendations.
261191 -
261192 - However, the paper does not provide any actual work product to convey
261193 - what was done, and illustrate application and cost/benefit
261194 -
261195 - No details are provided on any of the experiements showing what was
261196 - actually accomplished. ref DRT 1 1620  There is a web site...
261197 -
261198 -
261199 -      http://ecocyc.panbio.com:1555/class-subs?object=Genes
261200 -
261201 -
261202 - ...but access requires setting up an account, and this requires having
261203 - a gov or edu email address.  In any case, there is no reason examples
261204 - of work product form cannot be set out that do not disclose propritary
261205 - information, that demonstrate the generic benefits of the experiment.
261206 - ..
261207 - Results are given, for example
261208 -
261209 -    1.  Ontology Exchange Languages for Bioinformatics The underlying
261210 -        paradigms of Ontolingua and OML/CKML are subtly different -
261211 -        frames based vs. flow theory). Both require effort to learn the
261212 -        paradigm if you are not familiar with it. ref DRT 1 2772
261213 -
261214 -    2.  Ontolingua concepts mapped more closely to object databases and
261215 -        object oriented programming paradigms -- thus might be easier
261216 -        for typical bioinformaticist to learn. ref DRT 1 4070
261217 -
261218 -    3...
261219 -
261220 - There is no evidence offered showing any underlying paradigms, and
261221 - nothing to indicate the level of effort required to learn, or even
261222 - what needs to be learned.  No concept maps, no object databases are
261223 - shown or explained to assess what is represented.
261224 - ..
261225 - There is no explanation of how long it takes to create an
261226 - ontology, how much time is required to maintain it day-to-day, how
261227 - much time and skill is needed to use it, what kind of reports are
261228 - generated, and the kind and usefulness of reports supported by any of
261229 - the systems.
261230 -
261231 -     This reflects prospective hope that the capability will be useful
261232 -     in relation to the cost of using it, which was discussed on 000517
261233 -     reviewing Eric Armstrong's idea to use a system of catagories to
261234 -     manage information. ref SDS 53 1830
261235 - ..
261236 - There is an interesting table showing a matrix evaluation over
261237 - detailed properties of the representational expressiveness of
261238 - candidate languages, ref DRT 1 2940, which relates to Eric Armstrong's
261239 - planning on 000601 to provide Relational capabilities. ref SDS 61 4967
261240 -
261241 -
261242 -
261243 -
261244 -
261245 -
261246 -
261247 -
261248 -
261249 -
261250 -