FALDO

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Welcome to the mailing list that discusses the FALDO standard!

We aim to make position of biological sequence feature annotation semantically interchangeable.

Development of the ontology happens at https://github.com/OBF/FALDO/blob/master/faldo.ttl

0 selected

Jerven Bolleman

11/12/19

SPARQL over genome graphs stored in Odgi now supports FALDO

Dear Faldo users and co-developers, I just want to let you know that SPODGI[1] supports FALDO now.

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SPARQL over genome graphs stored in Odgi now supports FALDO

Dear Faldo users and co-developers, I just want to let you know that SPODGI[1] supports FALDO now.

11/12/19

Jerven Tjalling Bolleman, jerven....@sib.swiss2

12/13/18

Faldo:OneOfPosition add possiblePositions

The first part was accepted today On Tuesday, October 9, 2018 at 8:54:32 PM UTC+2, Jerven Tjalling

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Faldo:OneOfPosition add possiblePositions

The first part was accepted today On Tuesday, October 9, 2018 at 8:54:32 PM UTC+2, Jerven Tjalling

12/13/18

Jerven Bolleman

8/24/17

Moving the github repository for FALDO from personal to OBF

Dear Faldo users and co-developers, Chris Mungall raised the very good issue that currently the

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Moving the github repository for FALDO from personal to OBF

Dear Faldo users and co-developers, Chris Mungall raised the very good issue that currently the

8/24/17

Jerven Bolleman, Joachim Baran2

6/2/15

faldo:hasPosition instead of faldo:position https://github.com/JervenBolleman/FALDO/pull/23

Hi! I am fine with marking “position” as obsolete and introducing an equivalent “hasPosition”

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faldo:hasPosition instead of faldo:position https://github.com/JervenBolleman/FALDO/pull/23

Hi! I am fine with marking “position” as obsolete and introducing an equivalent “hasPosition”

6/2/15

4/6/15

Use of faldo:Region in for mapping chromosomal band positions

My more general question here is when can a feature being described be linked directly to a faldo:

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Use of faldo:Region in for mapping chromosomal band positions

My more general question here is when can a feature being described be linked directly to a faldo:

4/6/15

Jerven Bolleman

7/7/14

faldo:region property to redefine :InRangePosition

Hi Everyone, I had the following comment in my mail box for a while now. And I would like

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faldo:region property to redefine :InRangePosition

Hi Everyone, I had the following comment in my mail box for a while now. And I would like

7/7/14

Jerven Tjalling Bolleman

7/3/14

Documentation in HTML form and Content negotiation

Hi Everyone, I would like to announce that due to the excellent work by Toshiaki we now have HTML

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Documentation in HTML form and Content negotiation

Hi Everyone, I would like to announce that due to the excellent work by Toshiaki we now have HTML

7/3/14

Jerven Bolleman, Michel Dumontier2

6/23/14

N and C Terminal positions

Sounds good - this links up with SIO nicely (as subclasses of SIO concepts) http://semanticscience.

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N and C Terminal positions

Sounds good - this links up with SIO nicely (as subclasses of SIO concepts) http://semanticscience.

6/23/14

Chris Mungall, … Jerven Bolleman9

4/28/14

Using FALDO for basic genome features

Hi Chris, Michel, On 28 Apr 2014, at 20:15, Chris Mungall <cjmu...@lbl.gov> wrote: > >

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Using FALDO for basic genome features

Hi Chris, Michel, On 28 Apr 2014, at 20:15, Chris Mungall <cjmu...@lbl.gov> wrote: > >

4/28/14

Jerven Bolleman, … Chris Mungall5

4/27/14

Re: Mapping Faldo to SIO

>> Maybe something like this as an owl property chain will work. >> Could someone with

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Re: Mapping Faldo to SIO

>> Maybe something like this as an owl property chain will work. >> Could someone with

4/27/14

Jerven Bolleman

2/5/14

Submitted the article to the Journal of Biomedical Semantics

Hi Everyone, As promised the edition that was preprinted has been submitted to the Journal of

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Submitted the article to the Journal of Biomedical Semantics

Hi Everyone, As promised the edition that was preprinted has been submitted to the Journal of

2/5/14

Jerven Bolleman, … Joachim Baran7

2/4/14

Preprint submitted, would like to submit FALDO paper for peer review next tuesday (you then get individual approval request mails)

The names have been corrected now. When linking to the paper, it is best to use the DOI link Peter

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Preprint submitted, would like to submit FALDO paper for peer review next tuesday (you then get individual approval request mails)

The names have been corrected now. When linking to the paper, it is best to use the DOI link Peter

2/4/14

Jerven Bolleman, … Toshiaki Katayama10

1/30/14

大切 FALDO paper will go to preprint at 01:00 tonight (10:00 JST Tomorrow)

Hi Jerven, >> [TODO] >> I hope to replace the figure with an updated version (in

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大切 FALDO paper will go to preprint at 01:00 tonight (10:00 JST Tomorrow)

Hi Jerven, >> [TODO] >> I hope to replace the figure with an updated version (in

1/30/14

Jerven Bolleman, … Toshiaki Katayama7

1/29/14

Journal of Biomedical Semantic cover letter draft

2014/01/30 1:58、Toshiaki Katayama <toshiaki...@gmail.com> のメール： > 2014/01/29 23:47、

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Journal of Biomedical Semantic cover letter draft

2014/01/30 1:58、Toshiaki Katayama <toshiaki...@gmail.com> のメール： > 2014/01/29 23:47、

1/29/14

Jerven Bolleman

1/29/14

Suggested reviewers for journal submission

Hi Everyone, Please let me know personally (ie do not reply to list) if you know someone who would be

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Suggested reviewers for journal submission

Hi Everyone, Please let me know personally (ie do not reply to list) if you know someone who would be

1/29/14

Jerven Bolleman, … Peter Ansell11

1/28/14

UniProt uses FALDO

On 29 January 2014 09:30, Hilmar Lapp <hl...@drycafe.net> wrote: > > On Jan 28, 2014, at

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UniProt uses FALDO

On 29 January 2014 09:30, Hilmar Lapp <hl...@drycafe.net> wrote: > > On Jan 28, 2014, at

1/28/14

Jerven Bolleman

1/28/14

New paper, more figures less grammar errors

Hi All, Peter has been helping me finish the paper. I am really happy with it now :) Would people

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New paper, more figures less grammar errors

Hi All, Peter has been helping me finish the paper. I am really happy with it now :) Would people

1/28/14

Jerven Bolleman, … Peter Cock15

1/27/14

Re: Preprint time? (JSON-LD)

On Mon, Jan 27, 2014 at 6:52 PM, Joachim Baran <joachi...@gmail.com> wrote: > Hello,

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Re: Preprint time? (JSON-LD)

On Mon, Jan 27, 2014 at 6:52 PM, Joachim Baran <joachi...@gmail.com> wrote: > Hello,

1/27/14

Matthew Brush, Jerven Bolleman2

1/6/14

FALDO questions

Hi Matthew, On point 1. why is a gene not a region. The normal definition of gene is a unit of

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FALDO questions

Hi Matthew, On point 1. why is a gene not a region. The normal definition of gene is a unit of

1/6/14

Jerven Bolleman, … Joachim Baran10

12/29/13

Deadline 2 weeks from now (just before new year) submit paper

Hi! I just sent out a pull request with a few of my changes. I think the document needs quite a bit

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Deadline 2 weeks from now (just before new year) submit paper

Hi! I just sent out a pull request with a few of my changes. I think the document needs quite a bit

12/29/13

Peter Cock, … Jerven Bolleman4

12/9/13

Complex protein bond 'locations' in FALDO

On Mon, Dec 9, 2013 at 8:36 PM, Jerven Bolleman <m...@jerven.eu> wrote: > Hi Peter, Michel,

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Complex protein bond 'locations' in FALDO

On Mon, Dec 9, 2013 at 8:36 PM, Jerven Bolleman <m...@jerven.eu> wrote: > Hi Peter, Michel,

12/9/13

Jerven Bolleman, Peter Cock2

10/24/13

FALDO-paper examples collation

Hi Jerven, A single example DDBJ/GenBank file sounds good - but it may not be possible to find all

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FALDO-paper examples collation

Hi Jerven, A single example DDBJ/GenBank file sounds good - but it may not be possible to find all

10/24/13

cjmu...@lbl.gov, … Jerven Bolleman9

10/22/13

FALDO and JSON-LD

I see, there should be a context block that introduces shortcut and abbreviations. Will try plying

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FALDO and JSON-LD

I see, there should be a context block that introduces shortcut and abbreviations. Will try plying

10/22/13

Jerven Bolleman, Takatomo Fujisawa2

10/22/13

Fwd: FALDO-paper, affiliations and support statements as well as DDBJ examples!

Hi, Jerven I join in this mailing list using my old e-mail address. Could you re-invited to t...@nig.ac

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Fwd: FALDO-paper, affiliations and support statements as well as DDBJ examples!

Hi, Jerven I join in this mailing list using my old e-mail address. Could you re-invited to t...@nig.ac

10/22/13

Jerven Bolleman, … Hilmar Lapp5

10/22/13

Faldo-paper: Is an early release to http://arxiv.org/ an option?

Thanks Hilmar, saved me quite some time as I was looking at the bmc site. Regards, Jerven On Monday,

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Faldo-paper: Is an early release to http://arxiv.org/ an option?

Thanks Hilmar, saved me quite some time as I was looking at the bmc site. Regards, Jerven On Monday,

10/22/13

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