Issue 3690: Metadata for properties necessary?                                                                                                                                                                      (biomolecular-ftf)
Source:  (Mr. Philip Lijnzaad, p.lijnzaad@med.uu.nl)
Nature: Uncategorized Issue
Severity: 
Summary: 
- We have many properties lying around the spec; do we need a mechanism for
  getting meta data on this? I think we must have discussed in some detail,
  but the situation is quite pressing for SearchHit in particular: there we
  have hit_info, where prolly the most important piece of information is the
  goodness of the hit. What's the name of that: "score"? "p-value"?
  "quality"? What's it's type: float? double ? long? I realize that this is
  difficult to answer (otherwise we would have included it), but we are open
  to suggestions to make the standard a bit more precise in this respect
  (e.g., we're still willing to host a public repository kind-a-thing).
Resolution: accepted
Revised Text: Add the following text as a separate paragraph between paragraphs 2 and 3 in section 2.1.

Some of the entities described below use generic types such as Any or name-value pairs. It is deemed outside the scope of this
document to standardize the types of values that can be contained in these generic types.
Actions taken:
June 9, 2000: received issue
May 24, 2001: closed issue
Discussion: 

End of Annotations:=====
Date: Fri, 9 Jun 2000 15:39:29 +0100 (BST)
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From: Philip Lijnzaad <lijnzaad@ebi.ac.uk>
To: biomolecular-ftf@emerald.omg.org
cc: muilu@ebi.ac.uk
Subject: some issues ... 
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Hi all,

my apologies with being so awfully late on this, a few days before OMG
Oslo
(where I will not be going, sorry).



- We have many properties lying around the spec; do we need a
  mechanism for
  getting meta data on this? I think we must have discussed in some
  detail,
  but the situation is quite pressing for SearchHit in particular:
  there we
  have hit_info, where prolly the most important piece of information
  is the
  goodness of the hit. What's the name of that: "score"? "p-value"?
  "quality"? What's it's type: float? double ? long? I realize that
  this is
  difficult to answer (otherwise we would have included it), but we
  are open
  to suggestions to make the standard a bit more precise in this
  respect
  (e.g., we're still willing to host a public repository
  kind-a-thing). 

Date: Tue, 19 Sep 2000 12:26:43 +0100 (BST)
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From: Philip Lijnzaad <lijnzaad@ebi.ac.uk>
To: biomolecular-ftf@omg.org
cc: senger@ebi.ac.uk, muilu@ebi.ac.uk
Subject: Issue 3690: Metadata for properties necessary?
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The EBI proposes to resolve issue 3690  by adding the following text
as a
separate paragraph (between para 2 and 3) to section 2.1:

"Some of the entities described below use generic types such as
<bold>Any</bold> or name-value pairs. It is deemed outside the scope
of this
document to standardize the types of values that can be
contained in these generic types. An implementation may choose to
provide
access to such meta-data through other means. "

, or text to that effect. The idea is just to flag that we noticed the
issue,
but that the standard explicitly doesn't address it. 

                                                                      Philip
-- 
When C++ is your hammer, everything looks like a thumb. (Steven
Haflich)
-----------------------------------------------------------------------------
Philip Lijnzaad, lijnzaad@ebi.ac.uk \ European Bioinformatics
Institute,rm A2-24
+44 (0)1223 49 4639                 / Wellcome Trust Genome Campus,
Hinxton
+44 (0)1223 49 4468 (fax)           \ Cambridgeshire CB10 1SD,  GREAT
BRITAIN
PGP fingerprint: E1 03 BF 80 94 61 B6 FC  50 3D 1F 64 40 75 FB 53

Date: Tue, 19 Sep 2000 14:21:26 -0700
From: Scott Markel <smarkel@netgenics.com>
Organization: NetGenics, Inc.
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To: lijnzaad@ebi.ac.uk
CC: biomolecular-ftf@omg.org, senger@ebi.ac.uk, muilu@ebi.ac.uk
Subject: Re: Issue 3690: Metadata for properties necessary?
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Philip,

Philip Lijnzaad wrote:
> 
> The EBI proposes to resolve issue 3690  by adding the following text
as a
> separate paragraph (between para 2 and 3) to section 2.1:
> 
> "Some of the entities described below use generic types such as
> <bold>Any</bold> or name-value pairs. It is deemed outside the scope
of this
> document to standardize the types of values that can be
> contained in these generic types. An implementation may choose to
provide
> access to such meta-data through other means. "
> 
> , or text to that effect. The idea is just to flag that we noticed
the issue,
> but that the standard explicitly doesn't address it.

It's not so much a question of being out of scope as it is being a bit
late.  I think that, for example, we could still work out a mapping
between DDBJ/EMBL/GenBank features and the BSA annotation model if we
wanted to take the time.  It would make the spec more obviously
usable.

I'm okay with the paragraph you propose, but I might leave off the
last
sentence.

Scott

-- 
Scott Markel, Ph.D.       NetGenics, Inc.
smarkel@netgenics.com     4350 Executive Drive
Tel: 858 455 5223         Suite 260
FAX: 858 455 1388         San Diego, CA  92121

Date: Mon, 25 Sep 2000 13:35:12 +0100 (BST)
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From: Philip Lijnzaad <lijnzaad@ebi.ac.uk>
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Subject: Re: Issue 3690: Metadata for properties necessary?
Reply-to: lijnzaad@ebi.ac.uk
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Scott> It's not so much a question of being out of scope as it is
being a bit
Scott> late.  

well, if I remember correctly, I think we have tried a few times, but
came to
the conclusion that this was going to take time, and therefore sort of
judged
of scope.

Scott> I think that, for example, we could still work out a mapping
Scott> between DDBJ/EMBL/GenBank features and the BSA annotation model
if we
Scott> wanted to take the time.  It would make the spec more obviously
usable.

yes ...

Scott> I'm okay with the paragraph you propose, but I might leave off
the last
Scott> sentence.

OK. Cheers,
                                                                      Philip
-- 
When C++ is your hammer, everything looks like a thumb. (Steven
                                                                      Haflich)
-----------------------------------------------------------------------------
Philip Lijnzaad, lijnzaad@ebi.ac.uk \ European Bioinformatics
                                                                      Institute,rm
                                                                      A2-24
+44 (0)1223 49 4639                 / Wellcome Trust Genome Campus,
                                                                      Hinxton
+44 (0)1223 49 4468 (fax)           \ Cambridgeshire CB10 1SD,  GREAT
                                                                      BRITAIN
PGP fingerprint: E1 03 BF 80 94 61 B6 FC  50 3D 1F 64 40 75 FB 53

Date: Mon, 25 Sep 2000 11:21:53 -0700
From: Scott Markel <smarkel@netgenics.com>
Organization: NetGenics, Inc.
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CC: biomolecular-ftf@omg.org, senger@ebi.ac.uk, muilu@ebi.ac.uk
Subject: Re: Issue 3690: Metadata for properties necessary?
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Philip,

Philip Lijnzaad wrote:
> 
> Scott> It's not so much a question of being out of scope as it is
being a bit
> Scott> late.
> 
> well, if I remember correctly, I think we have tried a few times,
but came to
> the conclusion that this was going to take time, and therefore sort
of judged
> of scope.

Probably true.

> Scott> I think that, for example, we could still work out a mapping
> Scott> between DDBJ/EMBL/GenBank features and the BSA annotation
> model if we
> Scott> wanted to take the time.  It would make the spec more
> obviously usable.
> 
> yes ...
> 
> Scott> I'm okay with the paragraph you propose, but I might leave
> off the last
> Scott> sentence.
> 
> OK. Cheers,

Good.  Watch for this one in a new batch of proposed resolutions.

Scott

-- 
Scott Markel, Ph.D.       NetGenics, Inc.
smarkel@netgenics.com     4350 Executive Drive
Tel: 858 455 5223         Suite 260
FAX: 858 455 1388         San Diego, CA  92121