Bulk loader template question

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Bulk loader template question

Henry

I have a question about creating a bulk loader template.


I want to load a file with three columns: unique_record_name (say feature), cv_name (an ontology), and cvterm_name


The idea here is to associate ontology terms with a chado table via another table (feature_cvterm). It is important to specify the cv in case multiple ontologies contain cvterms with the same name.


However the options for “Type of Field” are mutually exclusive. That is - you cannot have “Data: A Field which maps to a column in the supplied file.” and “Record Referral: Fields which map to a record in another table” both selected.


I would like to be able to map a column of my file to a field (cvterm_name to the cvterm table) and I would like to perform a record referral to the cv_name (to specify the ontology). Is this possible with the bulk loader?


Thank you for your time,


Henry

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Re: Bulk loader template question

Kucheran, Lacey Sanderson
Hi Henry,

To do this you need a record to select the cv which uses the data type field for the cv.name and then a select record for the cvterm table where the cvterm.cv_id is of type record referral and points to the cv record.

So for more clarity you would end up with the following:
Record: CV (select)
  - Field: cv.name = column 2 (data)
Record CVTERM (select)
  - Field: cvterm.cv_id = First record (record referral)
  - Field: cvterm.name = column 1 (data)
Record: Feature (select)
  - Field: feature_uniquename = column 1 (data)
Record: Feature_cvterm (insert)
 - Field: feature_cvterm.cvterm_id = Second Record (record referral)
 - Field: feature_cvterm.feature = Third Record (record referral)

Note: The record referral is the foreign key field (cvterm.cv_id) which points to another bulk loader record where you actually define what record the foreign key should point to (record: cvterm).

Hope that helps!
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On February 1, 2016 at 10:07:21 AM, Nathan Henry ([hidden email]) wrote:

I have a question about creating a bulk loader template.


I want to load a file with three columns: unique_record_name (say feature), cv_name (an ontology), and cvterm_name


The idea here is to associate ontology terms with a chado table via another table (feature_cvterm). It is important to specify the cv in case multiple ontologies contain cvterms with the same name.


However the options for “Type of Field” are mutually exclusive. That is - you cannot have “Data: A Field which maps to a column in the supplied file.” and “Record Referral: Fields which map to a record in another table” both selected.


I would like to be able to map a column of my file to a field (cvterm_name to the cvterm table) and I would like to perform a record referral to the cv_name (to specify the ontology). Is this possible with the bulk loader?


Thank you for your time,


Henry
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Re: Bulk loader template question

Henry
Thanks for the quick response!

To clarify my understanding: when a record's mode is "select or select if duplicate", the record selected from the database will be contingent on all fields associated with that record. In the example you gave above this would mean that that the cvterm would be selected based on both the cvterm name and the cv_id provided. Is this correct?

Thanks for your time,

Henry

On Mon, Feb 1, 2016 at 11:40 AM, Kucheran, Lacey Sanderson <[hidden email]> wrote:
Hi Henry,

To do this you need a record to select the cv which uses the data type field for the cv.name and then a select record for the cvterm table where the cvterm.cv_id is of type record referral and points to the cv record.

So for more clarity you would end up with the following:
Record: CV (select)
  - Field: cv.name = column 2 (data)
Record CVTERM (select)
  - Field: cvterm.cv_id = First record (record referral)
  - Field: cvterm.name = column 1 (data)
Record: Feature (select)
  - Field: feature_uniquename = column 1 (data)
Record: Feature_cvterm (insert)
 - Field: feature_cvterm.cvterm_id = Second Record (record referral)
 - Field: feature_cvterm.feature = Third Record (record referral)

Note: The record referral is the foreign key field (cvterm.cv_id) which points to another bulk loader record where you actually define what record the foreign key should point to (record: cvterm).

Hope that helps!
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On February 1, 2016 at 10:07:21 AM, Nathan Henry ([hidden email]) wrote:

I have a question about creating a bulk loader template.


I want to load a file with three columns: unique_record_name (say feature), cv_name (an ontology), and cvterm_name


The idea here is to associate ontology terms with a chado table via another table (feature_cvterm). It is important to specify the cv in case multiple ontologies contain cvterms with the same name.


However the options for “Type of Field” are mutually exclusive. That is - you cannot have “Data: A Field which maps to a column in the supplied file.” and “Record Referral: Fields which map to a record in another table” both selected.


I would like to be able to map a column of my file to a field (cvterm_name to the cvterm table) and I would like to perform a record referral to the cv_name (to specify the ontology). Is this possible with the bulk loader?


Thank you for your time,


Henry
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Re: Bulk loader template question

Kucheran, Lacey Sanderson
Exactly :-)

~Lacey

PS. Select or select if duplicate is the same as just select. The select if duplicate is only helpful if your mode is insert.

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On February 1, 2016 at 11:54:48 AM, Nathan Henry ([hidden email]) wrote:

Thanks for the quick response!

To clarify my understanding: when a record's mode is "select or select if duplicate", the record selected from the database will be contingent on all fields associated with that record. In the example you gave above this would mean that that the cvterm would be selected based on both the cvterm name and the cv_id provided. Is this correct?

Thanks for your time,

Henry

On Mon, Feb 1, 2016 at 11:40 AM, Kucheran, Lacey Sanderson <[hidden email]> wrote:
Hi Henry,

To do this you need a record to select the cv which uses the data type field for the cv.name and then a select record for the cvterm table where the cvterm.cv_id is of type record referral and points to the cv record.

So for more clarity you would end up with the following:
Record: CV (select)
  - Field: cv.name = column 2 (data)
Record CVTERM (select)
  - Field: cvterm.cv_id = First record (record referral)
  - Field: cvterm.name = column 1 (data)
Record: Feature (select)
  - Field: feature_uniquename = column 1 (data)
Record: Feature_cvterm (insert)
 - Field: feature_cvterm.cvterm_id = Second Record (record referral)
 - Field: feature_cvterm.feature = Third Record (record referral)

Note: The record referral is the foreign key field (cvterm.cv_id) which points to another bulk loader record where you actually define what record the foreign key should point to (record: cvterm).

Hope that helps!
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On February 1, 2016 at 10:07:21 AM, Nathan Henry ([hidden email]) wrote:

I have a question about creating a bulk loader template.


I want to load a file with three columns: unique_record_name (say feature), cv_name (an ontology), and cvterm_name


The idea here is to associate ontology terms with a chado table via another table (feature_cvterm). It is important to specify the cv in case multiple ontologies contain cvterms with the same name.


However the options for “Type of Field” are mutually exclusive. That is - you cannot have “Data: A Field which maps to a column in the supplied file.” and “Record Referral: Fields which map to a record in another table” both selected.


I would like to be able to map a column of my file to a field (cvterm_name to the cvterm table) and I would like to perform a record referral to the cv_name (to specify the ontology). Is this possible with the bulk loader?


Thank you for your time,


Henry
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Re: Bulk loader template question

Henry
Great!

Thanks so much for your help!

Henry

On Mon, Feb 1, 2016 at 1:02 PM, Kucheran, Lacey Sanderson <[hidden email]> wrote:
Exactly :-)

~Lacey

PS. Select or select if duplicate is the same as just select. The select if duplicate is only helpful if your mode is insert.

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On February 1, 2016 at 11:54:48 AM, Nathan Henry ([hidden email]) wrote:

Thanks for the quick response!

To clarify my understanding: when a record's mode is "select or select if duplicate", the record selected from the database will be contingent on all fields associated with that record. In the example you gave above this would mean that that the cvterm would be selected based on both the cvterm name and the cv_id provided. Is this correct?

Thanks for your time,

Henry

On Mon, Feb 1, 2016 at 11:40 AM, Kucheran, Lacey Sanderson <[hidden email]> wrote:
Hi Henry,

To do this you need a record to select the cv which uses the data type field for the cv.name and then a select record for the cvterm table where the cvterm.cv_id is of type record referral and points to the cv record.

So for more clarity you would end up with the following:
Record: CV (select)
  - Field: cv.name = column 2 (data)
Record CVTERM (select)
  - Field: cvterm.cv_id = First record (record referral)
  - Field: cvterm.name = column 1 (data)
Record: Feature (select)
  - Field: feature_uniquename = column 1 (data)
Record: Feature_cvterm (insert)
 - Field: feature_cvterm.cvterm_id = Second Record (record referral)
 - Field: feature_cvterm.feature = Third Record (record referral)

Note: The record referral is the foreign key field (cvterm.cv_id) which points to another bulk loader record where you actually define what record the foreign key should point to (record: cvterm).

Hope that helps!
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On February 1, 2016 at 10:07:21 AM, Nathan Henry ([hidden email]) wrote:

I have a question about creating a bulk loader template.


I want to load a file with three columns: unique_record_name (say feature), cv_name (an ontology), and cvterm_name


The idea here is to associate ontology terms with a chado table via another table (feature_cvterm). It is important to specify the cv in case multiple ontologies contain cvterms with the same name.


However the options for “Type of Field” are mutually exclusive. That is - you cannot have “Data: A Field which maps to a column in the supplied file.” and “Record Referral: Fields which map to a record in another table” both selected.


I would like to be able to map a column of my file to a field (cvterm_name to the cvterm table) and I would like to perform a record referral to the cv_name (to specify the ontology). Is this possible with the bulk loader?


Thank you for your time,


Henry
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