March 2003 - tdwg-content - lists.tdwg.org

Re: Special states
by Joseph Poupin 18 Mar '03

18 Mar '03

just add a 'l' at the end of URL Kevin Thiele a écrit: >Can anybody else not access the Special States page as below, or is it just >me? > >----- Original Message ----- >From: "Steve Shattuck" <Steve.Shattuck(a)CSIRO.AU> >To: <TDWG-SDD(a)USOBI.ORG> >Sent: Tuesday, March 18, 2003 3:43 PM >Subject: Re: Special states > >

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Re: Special states
by Richard Pyle 17 Mar '03

17 Mar '03

You need to manually append the "l" (so that the URL ends in ".html", instead of ".htm"). The "l" was forced onto the next line in Steve's original message. Aloha, Rich Richard L. Pyle Natural Sciences Database Coordinator, Bishop Museum 1525 Bernice St., Honolulu, HI 96817 Ph: (808)848-4115, Fax: (808)847-8252 email: deepreef(a)bishopmuseum.org http://www.bishopmuseum.org/bishop/HBS/pylerichard.html "The opinions expressed are those of the sender, and not necessarily those of Bishop Museum." > -----Original Message----- > From: TDWG - Structure of Descriptive Data [mailto:TDWG-SDD@USOBI.ORG]On > Behalf Of Kevin Thiele > Sent: Monday, March 17, 2003 8:53 PM > To: TDWG-SDD(a)USOBI.ORG > Subject: Re: Special states > > > Can anybody else not access the Special States page as below, or > is it just > me? > > ----- Original Message ----- > From: "Steve Shattuck" <Steve.Shattuck(a)CSIRO.AU> > To: <TDWG-SDD(a)USOBI.ORG> > Sent: Tuesday, March 18, 2003 3:43 PM > Subject: Re: Special states > > > Hi All, > > I've had a look at the excellent "Special States" document > (http://160.45.63.11/Projects/TDWG-SDD/Docs/SDD_P_Data_SpecialStates.htm > l) put together by Gregor and a few comments are attached below. > > These comments are in several sections (with a few notes at the bottom). > Have a look at the first and last sections and the long second section > if you are expecially interested. This second section is pretty long > and rambles a bit, but covers a wide range of issues centred on Gregor's > document. Hopefully it will help move the SDD forward. > > Thanks, Steve > > ****************************************************************** > > SDD Special States > > At some level the details of the SDD structure are less important than > its content. This is because few (if any) consuming applications will > use SDD other than as a source of information, this information being > translated into application-specific formats for processing and > analysis. This requires mapping SDD items to local items and this can > be done for any given SDD structure. > > Taking this approach, I would make only one suggestion: generalize, > Generalize, GENERALIZE! What I mean is that the current Special States > document attempts to define all of the possible Special States that are > to be part of SDD and even goes so far as to exclude some potential > Special States. I would strongly suggest that SDD have a general method > for handling these, with at most a list of suggested Special States > rather than trying to be too restrictive. I firmly believe that it will > be extremely difficult (and short sighted) to try to define these as > part of the SDD Standard. The list of useful Special States is much > longer than the few suggested in the current document, and an extension > is even suggested at the end of the document, a "ToDo" Special State. > Many more can be thought of with little effort. > > This same difficulty (trying to be too specific) has arisen in related > activities within TDWG and has resulted in an unfortunate split among > participants. There are two camps within the specimen-based standards > group, one arguing for a complete description of specimens, the other > looking for a set of common items across most groups. The first group > has developed a "standard" with some 400 items while the second has > selected in the neighbourhood of 20 or so items. My impression is that > SDD is taking the first approach: study the problem long enough and the > entire universe of data items and their relationships can be documented. > I'm not confident this is possible. Biology is too diverse and needs > change too quickly to document all of life in any stable, meaningful and > useful way. We can provide a framework and make suggestions, but we > won't be successful if we try to dictate too narrowly. > > So my suggestion is that we focus on general needs, such as support for > Special States, but that we don't try to define other than at most a few > basic data items (such as general Special States). What we provide is a > mechanism to support this functionality with the ability to extend it in > a controlled and flexible way. > > > **************************************************** > > OK, this is where it gets ugly. I have a few specific comments on the > current Special States document, some relating to general issues, some > to specific comments. These are less important than the message above > and largely represent a slightly different perspective on SDD from the > one given in the current document. > > First, the scope of SDD. Currently SDD is trying to address three > separate and non-overlapping issues: (1) data, (2) business practices > and (3) application development. Data is the specific information items > under consideration, business practices are how we think of this items > and how we handle them, and applications are specific pieces of software > used by manage data items. The current Special States document mixes > these three areas, talking about data items, how people interpreter them > and how they might be displayed by a computer program. The first area > is clearly within the scope of SDD, the second possibly but only in a > very general, non-specific way, and the third is clearly outside SDD > (and well it should be). Bob made essentially this same comment when he > said that he thought "project management problems were not part of SDD." > We need to focus on DATA and nothing more. > > The second serious problem I have with Special States is that they > aren't "states" in the normal, taxonomic sense. Taxonomic "states" are > observations made about biological objects (be they taxa or specimens) > that are grouped together as "characters." We use "states" to describe > items. However, Special States aren't observable and aren't used to > describe items. > > What are "Special States"? They are a mix of two separate sets of > information. They document the status of data coding (for example > "unknown", "not interpretable" and "unfinished work") and they document > application-specific business rules (for example "use character default > state" - get the data based on a flag set for a specific state of this > character). These are fundamentally different things and show the > danger of mixing data, business practices and application development. > > Lack of appreciation for these differences as resulted in "use default" > being treated as a case of "data have not yet been entered" when in fact > a state has been clearly indicated (through a pointer): it's the default > state (however the data or application defines this) and is certainly > known. It's a user-interface shortcut used by an application to make > data entry quicker (in the opinion of an application developer!). The > end result is exactly the same as if the state had been entered directly > in the description (the taxon by character intersection, or what DELTA > calls the Attribute). > > This thinking results in some very complex processing being required by > consumers of SDD documents. For example, it is suggested that if a > description is null, then the "special state" called "use default" > should be inserted and that this "state" be set to "not yet evaluated." > This means that to interpret an SDD document you not only have to > understand the individual data items but also know the rules for > processing them (to know that if data is missing you need to insert a > special value and then look this value up in another list to translate > it into something meaningful). There must be a cleaner way to do this! > > The "unknown", "not interpretable" and similar "special states" are > another problem altogether. These "states" have nothing to do with > characters and everything to do with descriptions. This is why Mike > Dallwitz didn't include them as part of the Character List. I can > understand why you might want to treat these as "states" of characters > as this is the basic DELTA paradigm. However, there is no need to do > this and doing so only complicates things. For example, to tell if a > description has not been coded you'll need to get its state(s) and then > check their translations to see if any are "unknown", "not > interpretable" or any one of who knows how many other special > conditions. > > A much better way to implement this functionality would be to store an > "uncoded" flag with the description along with an (encoded or > text-based) explanation ("unknown", "not interpretable", "too lazy to > code this", "don't have proper specimens", "To Do" or what ever). This > is both direct and allows the explanation to change in a simple and > flexible way. > > These are the most serious and fundamental problems I have with the > current document. I would also add the following minor comments (some > of these expand on the above comments as well). > > The meaning of the DELTA "U" in attributes: It's stated in the document > that this means "attempts to research the information were made but > failed" and that "the state U in DELTA is also used for cases where data > are present, but the author is unable to interpret them in current > terminology." The DELTA documentation states simply that "A missing > attribute is equivalent to an attribute with pseudo-value U" and that > "If the state of the character is unknown, then the character is > omitted, or the state value coded as U." I can't find anything in the > DELTA documentation that gives a reason for the use of U or suggests > that "attempts to research the information were made but failed" or > anything similar. It would seem that DELTA treats nulls and U as the > same, nothing more. > > Remove all sections dealing with "performance", "user-interfaces" and > referring to "applications." These deal with specific software > developments and should not influence the SDD standard. > > Great care should be taken when developing "business rules" for > interpreting an SDD document. For example see the discussion starting > with "One frequent situation is that characters are added to the > terminology. Possible solutions to achieve a synchronization between > descriptions and a separate terminology in this case are:". It may be > important for SDD to document this situation but HOW it is dealt with is > up to individual applications and has little to do with the data itself > (which is the focus of SDD). The same problem occurs with the statement > "The omission of character coding in a description should be used to > express the "use default" state." This mixes data with processing. The > lack of data is simply that - it implies nothing more and NO assumptions > should be made about it. If the default state should be used then the > author needs to state this. > > What does "terminology" mean? It seems to be the character/character > state list but this is unclear. It might be good to develop a glossary > of terms so we all know what we're talking about. > > We also need to define "schema." My understanding is that a "schema" is > a model of the structure of the data and not the data itself. If you > add data you don't change the schema (assuming that this addition is > permitted by the schema - it's like adding rows to a database table - > the schema doesn't change, only the data). But at several points the > document says "... the case that the terminology is changing ("schema > evolution") is ..." or similar. This sounds like changes to the data > change the schema. Is this the general view of schema or am I on the > wrong track? > > The section discussing "Data have not yet been entered", "Data cannot be > entered" and "Data could have been entered but a deliberate decision was > made not to enter them" seems to mix unrelated cases and is a mess. The > options listed are (followed by my interpretation of their meaning): > 1) "Use character default state": Data is coded and is not missing (see > above). > 2) "Unfinished work": Data exists but has yet to be captured. > 3) "Not applicable": Data does not logically exist. > 4) "Unknown": Data exists but has yet to be captured. > 5) "Not interpretable": Data exists but has yet to be captured. > 6) "Out of scope": Data exists but has yet to be captured. > 7) "Do not need to score": Data is coded and is not missing. > The mix involves data that is being pointed to through a process (No. 1 > and 7), data that is impossible to collect (No. 3) and data that can be > collected but hasn't (for a variety of reasons) (No. 2, 4, 5 and 6). > Keep it simple by recording if data is absent and if it is, the reason. > Don't confuse it with application-specific short cuts ("Use default", > "Inherit/Compile from Parent/Children") or personal decisions made by an > author ("it's too hard to code", "this character is unimportant here", > "appropriate specimens are unavailable", etc). These are distinct > cases. > > There are a number of cases where attempts are made to develop lists of > conditions or situations. For example, it is asked "Should a general > 'cannot score' (for any kind of reason) be differentiated into" and then > three situations are listed. Again, generalise this into "uncoded" with > a text-based explanation ("observation method failed", "incomplete > specimen" or any one of a thousand other reasons). All the information > is captured and the system is rich enough to handle unforseen > situations. This approach also fits perfectly with the previous > example. > > There is a note that "a general method is planned (@but not yet > formalized!@) in SDD" and that "SDD is considering introducing computed > characters." We've been at this for at least 2 years now and there are > things that are "planned" or are "being considered" for SDD that we > don't know about?!?!? Or is there an overall planning document that I'm > not aware of? WE are SDD, SDD can't be "considering" things in > isolation. > > The entire discussion of inheritance and compilation (or what ever we > call it) needs to be though of in a fresh light. Again, the document > confuses data with process. For example, it's stated that "it is > desirable that the assumption [of inheritance/compilation] rather than > the inherited data are recorded". The author of the dataset MUST > present real data, not give a process to get to that data. Yes, the > author can tell us how they collected the data ("inherited from direct > parent", "compiled using Gouldes Statistic from all coded children", "by > reference to the default state for this character") but they also must > give us the data, not make us go look for it. The process of > inheritance/compilation is too complex to leave to chance and trying to > define exactly what it means is too error prone. I would suggest that > inheritance/compilation is an application-based activity, not a > fundamental aspect of the data. Again, give us the data and separately > tell us how it was derived, don't make us derive it ourselves. > > This exact same problem exists with "computed data." I don't see how or > why an SDD document can contain the value "CouldNotCompute" because the > "generator couldn't compute this". The "generator" is a piece of > software, not a data representation (which is what SDD is). > "CouldNotCompute" is an error message returned from an application and > it should never end up in an SDD document. Yet again, if you want to > explain how the data was generated, find, do it, but don't make us > calculate it, we don't know how. > > The discussion about "Not supported as special states, but supported > through modifiers" is good but, as above, describes descriptions and not > characters. That's why inheritance/compilation is included here. > > The statement "Special states express knowledge about why data for a > given character are missing in a description and thus make a statement > about the entire character" is interesting. It says that special states > are about a character in a description. The point I would make is that > they are primarily about the description, not the character. They say > nothing about the character's use for other items, and only relate to > this character in this taxon, and this is through the "description." So > let's focus this document on the description and only discuss the > character when it's appropriate. This is supported by the statement > that "DELTA does not define the special states in the "character list" > directive: they are implicitly present in each character." They are not > in the character list because the have little to do with characters. > They are in the DELTA attributes because they have everything to do with > descriptions. I'm sorry to say that the next statement shows the danger > of letting past developments influence current work (and I'm as guilty > as any): "When a new character is created, DeltaAccess automatically > creates the full set of special states." In BioLink we attach this > information to the description: you do it when you're coding the data, > not developing the character list. I don't know which way is better and > as noted above, it probably doesn't matter as each application will > translate the information into a local format anyway. What we DO need > to do is make sure the SDD format is expressive, flexible and as > application-neutral as possible (and ideally simple). > > Most of the discussion under "Relations between declarative character > dependency and special states" seems to deal with developing > applications rather than data representation and may well be outside > SDD. Sure, document that these dependencies exist and use them to > produce high-quality and internally consistent data, but do this at > application-level, not SDD-level. > > The same applies to "Responsibility for validation." SDD should be > about representing data in a standardized way, not about enforcing > taxonomic business rules or data quality standards. As SDD will be > represented in XML then this XML document must be well-formed and pass a > check with a DTD or XML-Schema checker. But SDD shouldn't be > responsible for checking the content of individual data items, that's > the job of authors and their applications. > > > ******************************************************** > > So, to summarize: > > SDD is about data and only data. These data include characters and > descriptions and (optionally) how these descriptions were developed and > their current status. > > SDD is not about process. Process information can be included but it is > optional and can be safely ignored without data loss. [I shouldn't have > to process a "use default data" statement to access a complete > description, the appropriate state(s) should be inserted into the > description when the SDD document is prepared with a note on how it was > derived.] > > SDD is not about applications. Discussions concerning user-interfaces > or processing methods should not be included. [How an application > manages and represents these data is completely independent of how SDD > represents the data.] > > > ******************************** > > Finally, I want to reconfirm that Gregor has done a fantastic job with > getting us this far and I support his efforts. My comments are more > about a different perspective rather than any serious flaw in logic. > Most of what is in the document is well presented and relevant to > managing taxonomic descriptions, I'm just not sure it is directly > related to the goals of SDD. > > And sorry for going on for so long. I'll sit down now. > > Steve > > Steve Shattuck > CSIRO Entomology > Steve.shattuck(a)csiro.au

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Special states
by Gregor Hagedorn 13 Mar '03

13 Mar '03

Before finishing the Paris minutes, I have just finished the last remaining bit from Brazil. On the last day we discussed special states, which was not really in the minutes released before Paris. I have written it as a separate document and have tried to work through some of the issues and scenarios we touched upon in Brazil. These include character scoping, default or implicit states, inheritance from taxonomic hierarchy, and a bit on character dependency. The result is a bit lengthy, but it did help _me_ a lot. I hope that the document can be pruned down when some parts can be moved elsewhere. I would love get your comments and feedback. Either sent them to the list, or if you have small corrections to help me you can write them into the document (Bob already did a first review helping to remove the worst logic and language errors!) and send it back to me. It is available at: http://160.45.63.11/Projects/TDWG- SDD/Docs/SDD_P_Data_SpecialStates.html Thanks Gregor ---------------------------------------------------------- Gregor Hagedorn (G.Hagedorn(a)bba.de) Institute for Plant Virology, Microbiology, and Biosafety Federal Research Center for Agriculture and Forestry (BBA) Koenigin-Luise-Str. 19 Tel: +49-30-8304-2220 14195 Berlin, Germany Fax: +49-30-8304-2203 Often wrong but never in doubt!

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Re: Correct term for collating/summarizing/consolidating/inferring from below
by unknown＠example.com 13 Mar '03

13 Mar '03

{Sorry for the delay in contributing this, I've been away the past few days.) In BioLink, we have the following options/commands: Compile with the options to: Compile Once Always Compile From Children Refresh Compile Inherit with the options to: Inherit Once Always Inherit From Parent Refresh Inherit We do this independently for each cell or attribute (that is, for each character for each taxon/item, or for each character by taxon/item intersection). This way you can build a full description by compiling some characters from children while inheriting other characters from the parent. We allow you to either regenerate these data automatically (by selecting the "Always Compile/Inherit from Children/Parent" command) or to create a static copy of the data so you can fine-tune it by manually inserting comments and clarifications (with the danger that changes to children/parents will not be reflected). Our hope is that by including the phrases "from children" and "from parent" in the commands that we can make the actions of these commands clear without having to resort to looking these terms up in the help files or, worse, a dictionary. Steve Shattuck CSIRO Entomology steve.shattuck(a)csiro.au

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Re: Correct term for collating/summarizing/consolidating/inferring from below
by ben moretti 12 Mar '03

12 Mar '03

On Wednesday, March 12, 2003, at 10:14 PM, Guillaume Rousse wrote: > Ainsi parlait Sauvenay Guillaume : >> Kevin Thiele wrote: >>> Consider this in the real world. If I have a number of descriptions >>> of >>> species, and from them I want to create a genus description, then I >>> would /collate/ the genus description from the species descriptions. >>> /Compile/ and /aggregate/ would also work, but I think collate works >>> better. I would call it "abstract". Rather like one creates an abstract data type in programming, or one can also create objects that are abstract representations, or models, of real-world things. Cheers Ben -- ben moretti bmoretti(a)chariot.net.au http://www.chariot.net.au/~bmoretti

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Re: Correct term for collating/summarizing/consolidating/inferring from below
by Gregor Hagedorn 12 Mar '03

12 Mar '03

> For me inference, induction, deduction sound like specific > methodologies, whereas collate, aggregate and compile correspond to > the generic process. In other words, you can collate/aggregate/compile > either by inference, by induction, or by deduction. I feel uneasy about calling the inheritance or deduction process an "aggregation" or "compilation". That may be a language point. Also I would think: induction = parent properties inferred from multiple children deduction = child properties inferred from (direct or remote) parents What then would your definition of "inference" as a third specific methodology be? > BTW, if the collate/aggregate/compile processs can be formalised and > at least expressed as a recomendation in the standard, it becomes > useless to store its result as it can be reproduced. Yes and no. Or Perhaps...? I think we need to explore this up/down topic on the taxonomic tree. Some information you want to inherit (i.e. child inherits from parten), other characters you don't because there is you know the character is too variable. You also want to contradict, but that is probably automatic if you enter data. However, if you enter data in a character downwards, you probably want the collation/Inheritance process to stop, the new data replace things for the entire character. In induction: You may have data about 100 specimen. 99 have states 1 or 2, 1 has state 3. You may want to remove state 3 from the aggregation process. Also: you may have a family where states 1 and 2 can be inferred by aggregation/induction/collation from below. You know however this family has also members with state 4 (which are otherwise not in you dataset). Should the aggregation break or should it be possible to add state 4 and keep 1 and 2 by aggregation/induction? Perhaps the process of making informed scientific decisions should be called the collation process. The algorithmic methods could be called aggregation = induction of knowledge inheritance = deduction of knowledge ??? Gregor ---------------------------------------------------------- Gregor Hagedorn (G.Hagedorn(a)bba.de) Institute for Plant Virology, Microbiology, and Biosafety Federal Research Center for Agriculture and Forestry (BBA) Koenigin-Luise-Str. 19 Tel: +49-30-8304-2220 14195 Berlin, Germany Fax: +49-30-8304-2203 Often wrong but never in doubt!

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Re: Correct term for collating/summarizing/consolidating/inferring from below
by Guillaume Rousse 12 Mar '03

12 Mar '03

Ainsi parlait Sauvenay Guillaume : > Kevin Thiele wrote: > > Consider this in the real world. If I have a number of descriptions of > > species, and from them I want to create a genus description, then I > > would /collate/ the genus description from the species descriptions. > > /Compile/ and /aggregate/ would also work, but I think collate works > > better. > > couldn't we call that induction? > here is a definition : > "Induction is the process of inference employed in "inductive logic". > A mode of reasoning that starts with specific facts and concludes > general hypotheses or theories" > > here, species descriptions are observed fact and genus description is > inducted > > and this term is less general than infer For me inference, induction, deduction sound like specific methodologies, whereas collate, aggregate and compile correspond to the generic process. In other words, you can collate/aggregate/compile either by inference, by induction, or by deduction. BTW, if the collate/aggregate/compile processs can be formalised and at least expressed as a recomendation in the standard, it becomes useless to store its result as it can be reproduced. -- When you finally buy enough memory, you will not have enough disk space. -- Murphy's Computer Laws n°3

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Re: Correct term for collating/summarizing/consolidating/inferring from below
by Kevin Thiele 12 Mar '03

12 Mar '03

Consider this in the real world. If I have a number of descriptions of species, and from them I want to create a genus description, then I would collate the genus description from the species descriptions. Compile and aggregate would also work, but I think collate works better. Cheers - k ----- Original Message ----- From: "Gregor Hagedorn" <G.Hagedorn(a)BBA.DE> To: <TDWG-SDD(a)USOBI.ORG> Sent: Wednesday, March 12, 2003 4:38 AM Subject: Correct term for collating/summarizing/consolidating/inferring from below | (While I am still working on the Paris minutes and related documents, | I would like to raise a minor point:) | | What term should we use for the process of inferring and collecting | information from multiple descriptions into a generated description? | Bob raised the point that "collation" may be inappropriate or | misleading. | | Please take a look at: | | http://160.45.63.11/Projects/TDWG- | SDD/Docs/SDD_P_InferenceCorrectTerm.html | | and send your comments to the list! | | thanks, Gregor | ---------------------------------------------------------- | Gregor Hagedorn (G.Hagedorn(a)bba.de) | Institute for Plant Virology, Microbiology, and Biosafety | Federal Research Center for Agriculture and Forestry (BBA) | Koenigin-Luise-Str. 19 Tel: +49-30-8304-2220 | 14195 Berlin, Germany Fax: +49-30-8304-2203 | | Often wrong but never in doubt!

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Re: Correct term for collating/summarizing/consolidating/inferring from below
by Peter Rauch 12 Mar '03

12 Mar '03

If "inducing" (not "inducting") a genus concept ("description") is unacceptable, then how about "synthesizing" a genus description ("concept") from the data garnered from the to-be-included species definitions (concepts)? (And, do other "related" genera/species influence one's thinking in the formulation of this new genus's concept/description too?) Peter On Wed, 12 Mar 2003, Sauvenay Guillaume wrote: > Kevin Thiele wrote: > > > Consider this in the real world. If I have a number of > > descriptions of species, and from them I want to create a > > genus description, then I would /collate/ the genus > > description from the species descriptions. /Compile/ and > > /aggregate/ would also work, but I think collate works > > better. > > couldn't we call that induction? > here is a definition : > "Induction is the process of inference employed in "inductive > logic". A mode of reasoning that starts with specific facts > and concludes general hypotheses or theories" > > here, species descriptions are observed fact and genus > description is inducted and this term is less general than > infer > > Guillaume Sauvenay

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Re: Correct term for collating/summarizing/consolidating/inferring from below
by Sauvenay Guillaume 12 Mar '03

12 Mar '03

Kevin Thiele wrote: > Consider this in the real world. If I have a number of descriptions of > species, and from them I want to create a genus description, then I > would /collate/ the genus description from the species descriptions. > /Compile/ and /aggregate/ would also work, but I think collate works > better. couldn't we call that induction? here is a definition : "Induction is the process of inference employed in "inductive logic". A mode of reasoning that starts with specific facts and concludes general hypotheses or theories" here, species descriptions are observed fact and genus description is inducted and this term is less general than infer Guillaume Sauvenay Université Pierre et Marie Curie CEB informatique et Systématique 12 rue Cuvier, esc B, 2e et 75005 Paris, France tel: 01.44.27.65.21 ou 01.44.27.65.22 fax: 01.44.27.65.60 http://lis.snv.jussieu.fr/~sauvenay

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