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SSARHERPS / SSAR-species-database

SSAR North American Common Names Database
http://ssarherps.org/cndb/
GNU General Public License v3.0
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Search on Taxon Notes field option in Advanced #48

Closed mkoo closed 9 years ago

mkoo commented 9 years ago

this may be the easiest way to find deprecated names as it will be in the Taxon notes (but open to other options as well).

tigerhawkvok commented 9 years ago

What about the dedicated field for it? I even have special types of searches run there...

atrox10 commented 9 years ago

Except these things were not deprecated in this round, they were deprecated in previous rounds (Masticophis was dropped and became Coluber) - so the only way to find out what happened to Masticophis is search on the species epithet only, or be able to search in the Notes fields.

On Mon, Jun 1, 2015 at 10:17 AM, Philip Kahn notifications@github.com wrote:

What about the dedicated field for it? I even have special types of searches run there...

— Reply to this email directly or view it on GitHub https://github.com/tigerhawkvok/SSAR-species-database/issues/48#issuecomment-107643925 .

Carol L. Spencer, Ph.D. Staff Curator of Herpetology & Researcher Museum of Vertebrate Zoology 3101 Valley Life Sciences Building University of California, Berkeley, CA, USA 94720-3160 atrox10@gmail.com and atrox@berkeley.edu 510-643-5778 /FAX: 510-643-8238

http://www.herpnet.org http://mvz.berkeley.edu/ http://www.vertnet.org

tigerhawkvok commented 9 years ago

Ah, the intent (which may not be practical) was for the deprecated field to have a list of deprecated names, however many.

Eg:

"Genus species":"Authority: year","Genus species":"Authority: year",...

So

"Masticophis flagellum":"John Smith: 1995","Othergenus otherspecies":"Joe Smith: 1950"

Does that not work? Extending the search to the note field makes me worried about diluting result relevance because of other words (or references to unrelated species, as the C. scutulatus ref in Mojave/Mohave entries) in the notes.

tigerhawkvok commented 9 years ago

I may be incompletely understanding the problem, or have inadequately labeled the Deprecated Scientific field.

atrox10 commented 9 years ago

Well maybe something to talk with Michelle. So with this model species that were recently deprecated (as in there are notes about it) would have to be added to the database as deprecated?

Like Masticophis flagellum deprecated and now Coluber flagellum?

Is that what you are saying?

On Mon, Jun 1, 2015 at 12:17 PM, Philip Kahn notifications@github.com wrote:

I may be incompletely understanding the problem, or have inadequately labeled the Deprecated Scientific field.

— Reply to this email directly or view it on GitHub https://github.com/tigerhawkvok/SSAR-species-database/issues/48#issuecomment-107675454 .

Carol L. Spencer, Ph.D. Staff Curator of Herpetology & Researcher Museum of Vertebrate Zoology 3101 Valley Life Sciences Building University of California, Berkeley, CA, USA 94720-3160 atrox10@gmail.com and atrox@berkeley.edu 510-643-5778 /FAX: 510-643-8238

http://www.herpnet.org http://mvz.berkeley.edu/ http://www.vertnet.org

tigerhawkvok commented 9 years ago

That's the way it's currently implemented / the system expects, yes. (This may need to be changed, and may not be reasonable, but that's how it checks for "old" names in searches right now)

tigerhawkvok commented 9 years ago

For clarity:

So for Coluber flagellum, I updated the record to included "Masticophis" in the deprecated field. Therefore, a search for "Masticophis flagellum" still returns Coluber flagellum.

image

See these notes in the README

Technical aside

(This part is mostly for @mkoo )

Here are some sample points where it specifically checks the deprecated zones (as per 3.ii in the README, under "Search Behaviour"):

459:

$result_vector = handleParamSearch($params,$loose,$boolean_type,"`deprecated_scientific` LIKE '%".$search."%'");
$method = "deprecated_scientific";

494:

# Always has to be a loose query
$method = "deprecated_scientific_raw";
$fallback = false;
$r = $db->doQuery(array("deprecated_scientific"=>$search),"*",$boolean_type,true,true,$order_by);
mkoo commented 9 years ago

ok great- I missed this is in the ReadMe. What are the other use cases to search on the Taxon Notes field? I still imagine that has usefulness but this will address the deprecated names in a slicker way.

On Mon, Jun 1, 2015 at 1:17 PM, Philip Kahn notifications@github.com wrote:

For clarity:

So for Coluber flagellum http://ssarherps.org/cndb/#Y29sdWJlcitmbGFnZWxsdW0mbG9vc2U9dHJ1ZQ, I updated the record to included "Masticophis" in the deprecated field. Therefore, a search for "Masticophis flagellum" http://ssarherps.org/cndb/#bWFzdGljb3BoaXMrZmxhZ2VsbHVtJmxvb3NlPXRydWU still returns Coluber flagellum.

[image: image] https://cloud.githubusercontent.com/assets/165937/7922362/8469f1d0-0860-11e5-8d55-46ea3ab52c96.png Technical aside

(This part is mostly for @mkoo https://github.com/mkoo )

Here are some sample points where it specifically checks the deprecated zones (as per 3.ii in the README https://github.com/tigerhawkvok/SSAR-species-database#search-behaviour, under "Search Behaviour"):

459: https://github.com/tigerhawkvok/SSAR-species-database/blob/master/commonnames_api.php#L459

$result_vector = handleParamSearch($params,$loose,$boolean_type,"deprecated_scientific LIKE '%".$search."%'");$method = "deprecated_scientific";

494: https://github.com/tigerhawkvok/SSAR-species-database/blob/master/commonnames_api.php#L494

Always has to be a loose query$method = "deprecated_scientific_raw";$fallback = false;$r = $db->doQuery(array("deprecated_scientific"=>$search),"*",$boolean_type,true,true,$order_by);

— Reply to this email directly or view it on GitHub https://github.com/tigerhawkvok/SSAR-species-database/issues/48#issuecomment-107694560 .

tigerhawkvok commented 9 years ago

I can't think of anything that wouldn't be contained in the note metadata, so to speak, but I'm open to suggestions.

I think that a notes search would need to be handled specially if it's not to do a crazy dilution of signal with noise, so I think the use case needs to come first (if any?)

mkoo commented 9 years ago

ok, since we're out of immediate use case examples, let's close this issue since deprecated species field is doing its intended job (ps. is authority and date required?)

On Mon, Jun 1, 2015 at 11:19 PM, Philip Kahn notifications@github.com wrote:

I can't think of anything that wouldn't be contained in the note metadata, so to speak, but I'm open to suggestions.

I think that a notes search would need to be handled specially if it's not to do a crazy dilution of signal with noise, so I think the use case needs to come first (if any?)

— Reply to this email directly or view it on GitHub https://github.com/tigerhawkvok/SSAR-species-database/issues/48#issuecomment-107823991 .