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Revision 5191

Added by Aaron Marcuse-Kubitza about 12 years ago

inputs/.TNRS/tnrs/map.csv: Use Name_matched_author/Name_matched_accepted_family instead of Author_matched/Family_matched because these fields are provided more often, due to being determined from the matched name itself rather than from the original string. This helps to fill in as many fields as possible. For accepted names (which scrub to themselves), this is especially important, because it adds the accepted name's family, which is not present in the input taxonomic name.

View differences:

inputs/.TNRS/tnrs/map.csv
5 5 
Name_matched,scientificName,,
6 6 
Name_matched_rank,taxonRank,,
7 7 
Name_score,OMIT,,
8 
Name_matched_author,OMIT,,"Contains author based on matched name, not author in original string, so not strictly from the original name"
8 
Name_matched_author,scientificNameAuthorship,,Contains author based on matched name
9 9 
Name_matched_url,OMIT,,
10 
Author_matched,scientificNameAuthorship,,
10 
Author_matched,OMIT,,Contains author in original string. Omitted because Name_matched_author provided more often.
11 11 
Author_score,OMIT,,
12 
Family_matched,family,,Contains any family in original string (uncommon)
12 
Family_matched,OMIT,,Contains family in original string (uncommon). Omitted because Name_matched_accepted_family provided more often.
13 13 
Family_score,OMIT,,
14 
Name_matched_accepted_family,OMIT,,"Contains family based on matched name, not family in original string, so not strictly from the original name"
14 
Name_matched_accepted_family,family,,Contains family based on matched name
15 15 
Genus_matched,genus,,
16 16 
Genus_score,OMIT,,
17 17 
Specific_epithet_matched,specificEpithet,,
inputs/.TNRS/tnrs/VegBIEN.csv
4 4 
Accepted_name,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/cond/_exists",
5 5 
Name_submitted,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/1",
6 6 
Name_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/1",
7 
Family_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/1",Contains any family in original string (uncommon)
7 
Name_matched_accepted_family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/1",Contains family based on matched name
8 8 
Genus_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/2",
9 9 
Specific_epithet_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/3",
10 10 
Infraspecific_epithet_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
11 11 
Infraspecific_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
12 12 
Name_matched_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
13 13 
Infraspecific_epithet_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2",
14 
Author_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/2",
15 
Author_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/author,
14 
Name_matched_author,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/2",Contains author based on matched name
15 
Name_matched_author,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/author,Contains author based on matched name
16 16 
Accepted_name_author,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/canon_taxonpath_id/taxonpath:[canon_taxonpath_id=0]/author,
17 17 
Accepted_name_family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/canon_taxonpath_id/taxonpath:[canon_taxonpath_id=0]/family,
18 18 
Accepted_name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/canon_taxonpath_id/taxonpath:[canon_taxonpath_id=0]/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/1,
......
21 21 
Accepted_name_author,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/canon_taxonpath_id/taxonpath:[canon_taxonpath_id=0]/identifyingtaxonomicname/_alt/2/_join_words/2,
22 22 
Accepted_name_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/canon_taxonpath_id/taxonpath:[canon_taxonpath_id=0]/subspecies/_alt/2/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
23 23 
Accepted_name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/canon_taxonpath_id/taxonpath:[canon_taxonpath_id=0]/taxonomicname,
24 
Family_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family,Contains any family in original string (uncommon)
24 
Name_matched_accepted_family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family,Contains family based on matched name
25 25 
Genus_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus,
26 26 
Specific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species,
27 27 
Infraspecific_epithet_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
......
34 34 
Accepted_name_species,,** No non-empty join mapping for OMIT ** Also contains genus. Omitted because Accepted_name contains more info.
35 35 
Accepted_name_url,,** No non-empty join mapping for OMIT **
36 36 
Annotations,,** No non-empty join mapping for OMIT **
37 
Author_matched,,** No non-empty join mapping for OMIT ** Contains author in original string. Omitted because Name_matched_author provided more often.
37 38 
Author_score,,** No non-empty join mapping for OMIT **
39 
Family_matched,,** No non-empty join mapping for OMIT ** Contains family in original string (uncommon). Omitted because Name_matched_accepted_family provided more often.
38 40 
Family_score,,** No non-empty join mapping for OMIT **
39 41 
Genus_score,,** No non-empty join mapping for OMIT **
40 42 
Infraspecific_epithet_2_matched,,** No non-empty join mapping for OMIT ** Need to parse the rank
41 43 
Infraspecific_epithet_2_score,,** No non-empty join mapping for OMIT **
42 44 
Infraspecific_epithet_score,,** No non-empty join mapping for OMIT **
43 45 
Infraspecific_rank_2,,** No non-empty join mapping for OMIT ** Need to parse the rank
44 
Name_matched_accepted_family,,"** No non-empty join mapping for OMIT ** Contains family based on matched name, not family in original string, so not strictly from the original name"
45 
Name_matched_author,,"** No non-empty join mapping for OMIT ** Contains author based on matched name, not author in original string, so not strictly from the original name"
46 46 
Name_matched_url,,** No non-empty join mapping for OMIT **
47 47 
Name_number,,** No non-empty join mapping for OMIT **
48 48 
Name_score,,** No non-empty join mapping for OMIT **
inputs/.TNRS/tnrs/test.xml.ref
19 19 
                                                            <1>$Name_matched</1>
20 20 
                                                            <2>
21 21 
                                                                <_join_words>
22 
                                                                    <1>$Family_matched</1>
22 
                                                                    <1>$Name_matched_accepted_family</1>
23 23 
                                                                    <2>$Genus_matched</2>
24 24 
                                                                    <3>$Specific_epithet_matched</3>
25 25 
                                                                    <5>
......
42 42 
                                                            </2>
43 43 
                                                        </_alt>
44 44 
                                                    </1>
45 
                                                    <2>$Author_matched</2>
45 
                                                    <2>$Name_matched_author</2>
46 46 
                                                </_join_words>
47 47 
                                            </2>
48 48 
                                        </_alt>
49 49 
                                    </identifyingtaxonomicname>
50 
                                    <author>$Author_matched</author>
50 
                                    <author>$Name_matched_author</author>
51 51 
                                    <canon_taxonpath_id>
52 52 
                                        <taxonpath>
53 53 
                                            <canon_taxonpath_id>0</canon_taxonpath_id>
......
67 67 
                                            <taxonomicname>$Accepted_name</taxonomicname>
68 68 
                                        </taxonpath>
69 69 
                                    </canon_taxonpath_id>
70 
                                    <family>$Family_matched</family>
70 
                                    <family>$Name_matched_accepted_family</family>
71 71 
                                    <genus>$Genus_matched</genus>
72 72 
                                    <species>$Specific_epithet_matched</species>
73 73 
                                    <subspecies>
inputs/.TNRS/tnrs/new_terms.csv
4 4 
Name_matched,scientificName,,
5 5 
Name_matched_rank,taxonRank,,
6 6 
Name_score,OMIT,,
7 
Name_matched_author,OMIT,,"Contains author based on matched name, not author in original string, so not strictly from the original name"
7 
Name_matched_author,scientificNameAuthorship,,Contains author based on matched name
8 8 
Name_matched_url,OMIT,,
9 
Author_matched,scientificNameAuthorship,,
9 
Author_matched,OMIT,,Contains author in original string. Omitted because Name_matched_author provided more often.
10 10 
Author_score,OMIT,,
11 
Family_matched,family,,Contains any family in original string (uncommon)
11 
Family_matched,OMIT,,Contains family in original string (uncommon). Omitted because Name_matched_accepted_family provided more often.
12 12 
Family_score,OMIT,,
13 
Name_matched_accepted_family,OMIT,,"Contains family based on matched name, not family in original string, so not strictly from the original name"
13 
Name_matched_accepted_family,family,,Contains family based on matched name
14 14 
Genus_matched,genus,,
15 15 
Genus_score,OMIT,,
16 16 
Specific_epithet_matched,specificEpithet,,

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