Revision 476
Added by Aaron Marcuse-Kubitza about 13 years ago
test/accepted_output/SALVIAS.organisms.VegBIEN.xml | ||
---|---|---|
19 | 19 |
<authorcode>1</authorcode> |
20 | 20 |
</plotevent> |
21 | 21 |
</plotevent_id> |
22 |
<collectiveobservation>
|
|
22 |
<aggregateoccurrence>
|
|
23 | 23 |
<count>1</count> |
24 | 24 |
<individualplant> |
25 | 25 |
<stemdiameter>662</stemdiameter> |
... | ... | |
27 | 27 |
<authorcode>8</authorcode> |
28 | 28 |
</stemobservation> |
29 | 29 |
</individualplant> |
30 |
</collectiveobservation>
|
|
30 |
</aggregateoccurrence>
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|
31 | 31 |
<taxondetermination> |
32 | 32 |
<role_id> |
33 | 33 |
<aux_role> |
... | ... | |
299 | 299 |
<authorcode>4</authorcode> |
300 | 300 |
</plotevent> |
301 | 301 |
</plotevent_id> |
302 |
<collectiveobservation>
|
|
302 |
<aggregateoccurrence>
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|
303 | 303 |
<count>1</count> |
304 | 304 |
<individualplant> |
305 | 305 |
<stemdiameter>215</stemdiameter> |
... | ... | |
307 | 307 |
<authorcode>91</authorcode> |
308 | 308 |
</stemobservation> |
309 | 309 |
</individualplant> |
310 |
</collectiveobservation>
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|
310 |
</aggregateoccurrence>
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|
311 | 311 |
<taxondetermination> |
312 | 312 |
<role_id> |
313 | 313 |
<aux_role> |
test/accepted_output/SALVIAS_db.organisms.VegBIEN.xml | ||
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12 | 12 |
</plot_id> |
13 | 13 |
</plotevent> |
14 | 14 |
</plotevent_id> |
15 |
<collectiveobservation>
|
|
15 |
<aggregateoccurrence>
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|
16 | 16 |
<count>1</count> |
17 |
</collectiveobservation>
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|
17 |
</aggregateoccurrence>
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|
18 | 18 |
<taxondetermination> |
19 | 19 |
<role_id> |
20 | 20 |
<aux_role> |
... | ... | |
288 | 288 |
</plot_id> |
289 | 289 |
</plotevent> |
290 | 290 |
</plotevent_id> |
291 |
<collectiveobservation>
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|
291 |
<aggregateoccurrence>
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|
292 | 292 |
<count>1</count> |
293 |
</collectiveobservation>
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|
293 |
</aggregateoccurrence>
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|
294 | 294 |
<taxondetermination> |
295 | 295 |
<role_id> |
296 | 296 |
<aux_role> |
test/accepted_output/NYBG.organisms.VegBIEN.xml | ||
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42 | 42 |
<authorcode>816590</authorcode> |
43 | 43 |
</plotevent> |
44 | 44 |
</plotevent_id> |
45 |
<collectiveobservation>
|
|
45 |
<aggregateoccurrence>
|
|
46 | 46 |
<individualplant> |
47 | 47 |
<stemobservation> |
48 | 48 |
<definedvalue fkey="tableRecord_ID"> |
... | ... | |
68 | 68 |
</stemobservation> |
69 | 69 |
</individualplant> |
70 | 70 |
<count>1</count> |
71 |
</collectiveobservation>
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|
71 |
</aggregateoccurrence>
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|
72 | 72 |
<taxondetermination> |
73 | 73 |
<role_id> |
74 | 74 |
<aux_role> |
... | ... | |
529 | 529 |
</plantname> |
530 | 530 |
</plantname_id> |
531 | 531 |
</taxondetermination> |
532 |
<collectiveobservation>
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|
532 |
<aggregateoccurrence>
|
|
533 | 533 |
<count>1</count> |
534 |
</collectiveobservation>
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|
534 |
</aggregateoccurrence>
|
|
535 | 535 |
</taxonoccurrence> |
536 | 536 |
</VegBIEN> |
inputs/SALVIAS/map.VegBIEN.organisms.csv | ||
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1 | 1 |
SALVIAS:plotObservations,VegBIEN:/taxonoccurrence,Comments |
2 | 2 |
PlotID,/*_id/plotevent/authorcode/_alt/1,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above." |
3 | 3 |
PlotCode,"/*_id/plotevent/{*_id/plot:[confidentialitystatus=0]/authorcode/_alt/2,authorcode/_alt/2}","Brad: Same as plotCode, above" |
4 |
NoInd,/collectiveobservation/count/_alt/1,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."
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|
5 |
cover_percent,/collectiveobservation/cover,
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|
6 |
intercept_cm,"/collectiveobservation/definedvalue[*_id/userdefined[tablename=collectiveobservation,userdefinedname=interceptCm]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
|
|
7 |
temp_dbh,/collectiveobservation/individualplant/stemdiameter,
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|
8 |
height_m,/collectiveobservation/individualplant/stemheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
|
|
9 |
tag2,/collectiveobservation/individualplant/stemobservation/authorcode/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
|
|
10 |
tag1,/collectiveobservation/individualplant/stemobservation/authorcode/_alt/2,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
|
|
11 |
ht_first_branch_m,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=heightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
|
|
12 |
x_position,/collectiveobservation/individualplant/stemobservation/stemxposition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX."
|
|
13 |
y_position,/collectiveobservation/individualplant/stemobservation/stemyposition,Brad: See comment above for x_position
|
|
4 |
NoInd,/aggregateoccurrence/count/_alt/1,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."
|
|
5 |
cover_percent,/aggregateoccurrence/cover,
|
|
6 |
intercept_cm,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
|
|
7 |
temp_dbh,/aggregateoccurrence/individualplant/stemdiameter,
|
|
8 |
height_m,/aggregateoccurrence/individualplant/stemheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
|
|
9 |
tag2,/aggregateoccurrence/individualplant/stemobservation/authorcode/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
|
|
10 |
tag1,/aggregateoccurrence/individualplant/stemobservation/authorcode/_alt/2,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
|
|
11 |
ht_first_branch_m,"/aggregateoccurrence/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=heightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
|
|
12 |
x_position,/aggregateoccurrence/individualplant/stemobservation/stemxposition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX."
|
|
13 |
y_position,/aggregateoccurrence/individualplant/stemobservation/stemyposition,Brad: See comment above for x_position
|
|
14 | 14 |
census_date,/taxondetermination[role_id/aux_role/rolecode=collector]/collectiondate/_date/date, |
15 | 15 |
coll_number,/taxondetermination[role_id/aux_role/rolecode=collector]/collectionnumber,Brad: Incorrect. Map instead as for voucher_string |
16 | 16 |
coll_firstname,"/taxondetermination[role_id/aux_role/rolecode=collector]/collector_id/party/{givenname/_namePart/first,middlename/_namePart/last}",Brad: See comment above |
... | ... | |
29 | 29 |
infra_ep_1,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=""Computer (automated)"",originaldetermination=false,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname/_name/last,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname/_name/last}", |
30 | 30 |
OrigFamily,"/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}",Brad: OMIT |
31 | 31 |
OrigSpecies,"/{taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname},taxondetermination[role_id/aux_role/rolecode=collector]/*_id/*/plantname/_alt/2}",Brad: OMIT |
32 |
PlotObsID,":[collectiveobservation/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/museumaccessionnumber,*_id/plotevent/authorcode/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/authorcode/_alt/3}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
|
32 |
PlotObsID,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/museumaccessionnumber,*_id/plotevent/authorcode/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/authorcode/_alt/3}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
schemas/vegbien_empty.sql | ||
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1 | 1 |
TRUNCATE address CASCADE; |
2 |
TRUNCATE aggregateoccurrence CASCADE; |
|
2 | 3 |
TRUNCATE aux_role CASCADE; |
3 | 4 |
TRUNCATE classcontributor CASCADE; |
4 | 5 |
TRUNCATE collection CASCADE; |
5 |
TRUNCATE collectiveobservation CASCADE; |
|
6 | 6 |
TRUNCATE commclass CASCADE; |
7 | 7 |
TRUNCATE commconcept CASCADE; |
8 | 8 |
TRUNCATE commcorrelation CASCADE; |
schemas/vegbien.sql | ||
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66 | 66 |
|
67 | 67 |
|
68 | 68 |
-- |
69 |
-- Name: aggregateoccurrence; Type: TABLE; Schema: public; Owner: -; Tablespace: |
|
70 |
-- |
|
71 |
|
|
72 |
CREATE TABLE aggregateoccurrence ( |
|
73 |
aggregateoccurrence_id integer NOT NULL, |
|
74 |
taxonoccurrence_id integer NOT NULL, |
|
75 |
taxonbin_id integer, |
|
76 |
cover double precision, |
|
77 |
basalarea double precision, |
|
78 |
biomass double precision, |
|
79 |
inferencearea double precision, |
|
80 |
stratumbase double precision, |
|
81 |
stratumheight double precision, |
|
82 |
emb_aggregateoccurrence integer, |
|
83 |
covercode character varying(10), |
|
84 |
count integer NOT NULL |
|
85 |
); |
|
86 |
|
|
87 |
|
|
88 |
-- |
|
89 |
-- Name: aggregateoccurrence_aggregateoccurrence_id_seq; Type: SEQUENCE; Schema: public; Owner: - |
|
90 |
-- |
|
91 |
|
|
92 |
CREATE SEQUENCE aggregateoccurrence_aggregateoccurrence_id_seq |
|
93 |
START WITH 1 |
|
94 |
INCREMENT BY 1 |
|
95 |
NO MINVALUE |
|
96 |
NO MAXVALUE |
|
97 |
CACHE 1; |
|
98 |
|
|
99 |
|
|
100 |
-- |
|
101 |
-- Name: aggregateoccurrence_aggregateoccurrence_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: - |
|
102 |
-- |
|
103 |
|
|
104 |
ALTER SEQUENCE aggregateoccurrence_aggregateoccurrence_id_seq OWNED BY aggregateoccurrence.aggregateoccurrence_id; |
|
105 |
|
|
106 |
|
|
107 |
-- |
|
69 | 108 |
-- Name: aux_role; Type: TABLE; Schema: public; Owner: -; Tablespace: |
70 | 109 |
-- |
71 | 110 |
|
... | ... | |
169 | 208 |
SET default_with_oids = true; |
170 | 209 |
|
171 | 210 |
-- |
172 |
-- Name: collectiveobservation; Type: TABLE; Schema: public; Owner: -; Tablespace: |
|
173 |
-- |
|
174 |
|
|
175 |
CREATE TABLE collectiveobservation ( |
|
176 |
collectiveobservation_id integer NOT NULL, |
|
177 |
taxonoccurrence_id integer NOT NULL, |
|
178 |
taxonbin_id integer, |
|
179 |
cover double precision, |
|
180 |
basalarea double precision, |
|
181 |
biomass double precision, |
|
182 |
inferencearea double precision, |
|
183 |
stratumbase double precision, |
|
184 |
stratumheight double precision, |
|
185 |
emb_collectiveobservation integer, |
|
186 |
covercode character varying(10), |
|
187 |
count integer NOT NULL |
|
188 |
); |
|
189 |
|
|
190 |
|
|
191 |
-- |
|
192 |
-- Name: collectiveobservation_collectiveobservation_id_seq; Type: SEQUENCE; Schema: public; Owner: - |
|
193 |
-- |
|
194 |
|
|
195 |
CREATE SEQUENCE collectiveobservation_collectiveobservation_id_seq |
|
196 |
START WITH 1 |
|
197 |
INCREMENT BY 1 |
|
198 |
NO MINVALUE |
|
199 |
NO MAXVALUE |
|
200 |
CACHE 1; |
|
201 |
|
|
202 |
|
|
203 |
-- |
|
204 |
-- Name: collectiveobservation_collectiveobservation_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: - |
|
205 |
-- |
|
206 |
|
|
207 |
ALTER SEQUENCE collectiveobservation_collectiveobservation_id_seq OWNED BY collectiveobservation.collectiveobservation_id; |
|
208 |
|
|
209 |
|
|
210 |
-- |
|
211 | 211 |
-- Name: commclass; Type: TABLE; Schema: public; Owner: -; Tablespace: |
212 | 212 |
-- |
213 | 213 |
|
... | ... | |
1082 | 1082 |
|
1083 | 1083 |
CREATE TABLE individualplant ( |
1084 | 1084 |
individualplant_id integer NOT NULL, |
1085 |
collectiveobservation_id integer NOT NULL,
|
|
1085 |
aggregateoccurrence_id integer NOT NULL,
|
|
1086 | 1086 |
stemdiameter double precision, |
1087 | 1087 |
stemdiameteraccuracy double precision, |
1088 | 1088 |
stemheight double precision, |
... | ... | |
3061 | 3061 |
|
3062 | 3062 |
|
3063 | 3063 |
-- |
3064 |
-- Name: aggregateoccurrence_id; Type: DEFAULT; Schema: public; Owner: - |
|
3065 |
-- |
|
3066 |
|
|
3067 |
ALTER TABLE aggregateoccurrence ALTER COLUMN aggregateoccurrence_id SET DEFAULT nextval('aggregateoccurrence_aggregateoccurrence_id_seq'::regclass); |
|
3068 |
|
|
3069 |
|
|
3070 |
-- |
|
3064 | 3071 |
-- Name: role_id; Type: DEFAULT; Schema: public; Owner: - |
3065 | 3072 |
-- |
3066 | 3073 |
|
... | ... | |
3082 | 3089 |
|
3083 | 3090 |
|
3084 | 3091 |
-- |
3085 |
-- Name: collectiveobservation_id; Type: DEFAULT; Schema: public; Owner: - |
|
3086 |
-- |
|
3087 |
|
|
3088 |
ALTER TABLE collectiveobservation ALTER COLUMN collectiveobservation_id SET DEFAULT nextval('collectiveobservation_collectiveobservation_id_seq'::regclass); |
|
3089 |
|
|
3090 |
|
|
3091 |
-- |
|
3092 | 3092 |
-- Name: commclass_id; Type: DEFAULT; Schema: public; Owner: - |
3093 | 3093 |
-- |
3094 | 3094 |
|
... | ... | |
3615 | 3615 |
|
3616 | 3616 |
|
3617 | 3617 |
-- |
3618 |
-- Name: aux_role_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
|
|
3618 |
-- Name: aggregateoccurrence_keys; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
|
|
3619 | 3619 |
-- |
3620 | 3620 |
|
3621 |
ALTER TABLE ONLY aux_role
|
|
3622 |
ADD CONSTRAINT aux_role_pkey PRIMARY KEY (role_id);
|
|
3621 |
ALTER TABLE ONLY aggregateoccurrence
|
|
3622 |
ADD CONSTRAINT aggregateoccurrence_keys UNIQUE (taxonoccurrence_id, taxonbin_id);
|
|
3623 | 3623 |
|
3624 | 3624 |
|
3625 | 3625 |
-- |
3626 |
-- Name: classcontributor_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
|
|
3626 |
-- Name: aggregateoccurrence_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
|
|
3627 | 3627 |
-- |
3628 | 3628 |
|
3629 |
ALTER TABLE ONLY classcontributor
|
|
3630 |
ADD CONSTRAINT classcontributor_pkey PRIMARY KEY (classcontributor_id);
|
|
3629 |
ALTER TABLE ONLY aggregateoccurrence
|
|
3630 |
ADD CONSTRAINT aggregateoccurrence_pkey PRIMARY KEY (aggregateoccurrence_id);
|
|
3631 | 3631 |
|
3632 | 3632 |
|
3633 | 3633 |
-- |
3634 |
-- Name: collection_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
|
|
3634 |
-- Name: aux_role_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
|
|
3635 | 3635 |
-- |
3636 | 3636 |
|
3637 |
ALTER TABLE ONLY collection
|
|
3638 |
ADD CONSTRAINT collection_pkey PRIMARY KEY (collection_id);
|
|
3637 |
ALTER TABLE ONLY aux_role
|
|
3638 |
ADD CONSTRAINT aux_role_pkey PRIMARY KEY (role_id);
|
|
3639 | 3639 |
|
3640 | 3640 |
|
3641 | 3641 |
-- |
3642 |
-- Name: collectiveobservation_keys; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
|
|
3642 |
-- Name: classcontributor_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
|
|
3643 | 3643 |
-- |
3644 | 3644 |
|
3645 |
ALTER TABLE ONLY collectiveobservation
|
|
3646 |
ADD CONSTRAINT collectiveobservation_keys UNIQUE (taxonoccurrence_id, taxonbin_id);
|
|
3645 |
ALTER TABLE ONLY classcontributor
|
|
3646 |
ADD CONSTRAINT classcontributor_pkey PRIMARY KEY (classcontributor_id);
|
|
3647 | 3647 |
|
3648 | 3648 |
|
3649 | 3649 |
-- |
3650 |
-- Name: collectiveobservation_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
|
|
3650 |
-- Name: collection_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace: |
|
3651 | 3651 |
-- |
3652 | 3652 |
|
3653 |
ALTER TABLE ONLY collectiveobservation
|
|
3654 |
ADD CONSTRAINT collectiveobservation_pkey PRIMARY KEY (collectiveobservation_id);
|
|
3653 |
ALTER TABLE ONLY collection |
|
3654 |
ADD CONSTRAINT collection_pkey PRIMARY KEY (collection_id);
|
|
3655 | 3655 |
|
3656 | 3656 |
|
3657 | 3657 |
-- |
... | ... | |
3891 | 3891 |
-- |
3892 | 3892 |
|
3893 | 3893 |
ALTER TABLE ONLY individualplant |
3894 |
ADD CONSTRAINT individualplant_keys UNIQUE (collectiveobservation_id, authorcode);
|
|
3894 |
ADD CONSTRAINT individualplant_keys UNIQUE (aggregateoccurrence_id, authorcode);
|
|
3895 | 3895 |
|
3896 | 3896 |
|
3897 | 3897 |
-- |
... | ... | |
4397 | 4397 |
|
4398 | 4398 |
|
4399 | 4399 |
-- |
4400 |
-- Name: aux_role_accessioncode_index; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
4400 |
-- Name: aggregateoccurrence_taxonbin_id_x; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
4401 | 4401 |
-- |
4402 | 4402 |
|
4403 |
CREATE UNIQUE INDEX aux_role_accessioncode_index ON aux_role USING btree (accessioncode);
|
|
4403 |
CREATE INDEX aggregateoccurrence_taxonbin_id_x ON aggregateoccurrence USING btree (taxonbin_id);
|
|
4404 | 4404 |
|
4405 | 4405 |
|
4406 | 4406 |
-- |
4407 |
-- Name: classcontributor_commclass_id_x; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
4407 |
-- Name: aggregateoccurrence_taxonoccurrence_id_x; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
4408 | 4408 |
-- |
4409 | 4409 |
|
4410 |
CREATE INDEX classcontributor_commclass_id_x ON classcontributor USING btree (commclass_id);
|
|
4410 |
CREATE INDEX aggregateoccurrence_taxonoccurrence_id_x ON aggregateoccurrence USING btree (taxonoccurrence_id);
|
|
4411 | 4411 |
|
4412 | 4412 |
|
4413 | 4413 |
-- |
4414 |
-- Name: classcontributor_party_id_x; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
4414 |
-- Name: aux_role_accessioncode_index; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
4415 | 4415 |
-- |
4416 | 4416 |
|
4417 |
CREATE INDEX classcontributor_party_id_x ON classcontributor USING btree (party_id);
|
|
4417 |
CREATE UNIQUE INDEX aux_role_accessioncode_index ON aux_role USING btree (accessioncode);
|
|
4418 | 4418 |
|
4419 | 4419 |
|
4420 | 4420 |
-- |
4421 |
-- Name: classcontributor_role_id_x; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
4421 |
-- Name: classcontributor_commclass_id_x; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
4422 | 4422 |
-- |
4423 | 4423 |
|
4424 |
CREATE INDEX classcontributor_role_id_x ON classcontributor USING btree (role_id);
|
|
4424 |
CREATE INDEX classcontributor_commclass_id_x ON classcontributor USING btree (commclass_id);
|
|
4425 | 4425 |
|
4426 | 4426 |
|
4427 | 4427 |
-- |
4428 |
-- Name: collectiveobservation_taxonbin_id_x; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
4428 |
-- Name: classcontributor_party_id_x; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
4429 | 4429 |
-- |
4430 | 4430 |
|
4431 |
CREATE INDEX collectiveobservation_taxonbin_id_x ON collectiveobservation USING btree (taxonbin_id);
|
|
4431 |
CREATE INDEX classcontributor_party_id_x ON classcontributor USING btree (party_id);
|
|
4432 | 4432 |
|
4433 | 4433 |
|
4434 | 4434 |
-- |
4435 |
-- Name: collectiveobservation_taxonoccurrence_id_x; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
4435 |
-- Name: classcontributor_role_id_x; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
4436 | 4436 |
-- |
4437 | 4437 |
|
4438 |
CREATE INDEX collectiveobservation_taxonoccurrence_id_x ON collectiveobservation USING btree (taxonoccurrence_id);
|
|
4438 |
CREATE INDEX classcontributor_role_id_x ON classcontributor USING btree (role_id);
|
|
4439 | 4439 |
|
4440 | 4440 |
|
4441 | 4441 |
-- |
... | ... | |
4670 | 4670 |
|
4671 | 4671 |
|
4672 | 4672 |
-- |
4673 |
-- Name: emb_classcontributor_idx; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
4673 |
-- Name: emb_aggregateoccurrence_idx; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
4674 | 4674 |
-- |
4675 | 4675 |
|
4676 |
CREATE INDEX emb_classcontributor_idx ON classcontributor USING btree (emb_classcontributor);
|
|
4676 |
CREATE INDEX emb_aggregateoccurrence_idx ON aggregateoccurrence USING btree (emb_aggregateoccurrence);
|
|
4677 | 4677 |
|
4678 | 4678 |
|
4679 | 4679 |
-- |
4680 |
-- Name: emb_collectiveobservation_idx; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
4680 |
-- Name: emb_classcontributor_idx; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
4681 | 4681 |
-- |
4682 | 4682 |
|
4683 |
CREATE INDEX emb_collectiveobservation_idx ON collectiveobservation USING btree (emb_collectiveobservation);
|
|
4683 |
CREATE INDEX emb_classcontributor_idx ON classcontributor USING btree (emb_classcontributor);
|
|
4684 | 4684 |
|
4685 | 4685 |
|
4686 | 4686 |
-- |
... | ... | |
4796 | 4796 |
|
4797 | 4797 |
|
4798 | 4798 |
-- |
4799 |
-- Name: individualplant_collectiveobservation_id_x; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
4799 |
-- Name: individualplant_aggregateoccurrence_id_x; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
4800 | 4800 |
-- |
4801 | 4801 |
|
4802 |
CREATE INDEX individualplant_collectiveobservation_id_x ON individualplant USING btree (collectiveobservation_id);
|
|
4802 |
CREATE INDEX individualplant_aggregateoccurrence_id_x ON individualplant USING btree (aggregateoccurrence_id);
|
|
4803 | 4803 |
|
4804 | 4804 |
|
4805 | 4805 |
-- |
... | ... | |
5612 | 5612 |
|
5613 | 5613 |
|
5614 | 5614 |
-- |
5615 |
-- Name: r1classcontributor_commclass_id; Type: FK CONSTRAINT; Schema: public; Owner: -
|
|
5615 |
-- Name: r1aggregateoccurrence_taxonoccurrence_id; Type: FK CONSTRAINT; Schema: public; Owner: -
|
|
5616 | 5616 |
-- |
5617 | 5617 |
|
5618 |
ALTER TABLE ONLY classcontributor
|
|
5619 |
ADD CONSTRAINT r1classcontributor_commclass_id FOREIGN KEY (commclass_id) REFERENCES commclass(commclass_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
5618 |
ALTER TABLE ONLY aggregateoccurrence
|
|
5619 |
ADD CONSTRAINT r1aggregateoccurrence_taxonoccurrence_id FOREIGN KEY (taxonoccurrence_id) REFERENCES taxonoccurrence(taxonoccurrence_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
5620 | 5620 |
|
5621 | 5621 |
|
5622 | 5622 |
-- |
5623 |
-- Name: r1collectiveobservation_taxonoccurrence_id; Type: FK CONSTRAINT; Schema: public; Owner: -
|
|
5623 |
-- Name: r1classcontributor_commclass_id; Type: FK CONSTRAINT; Schema: public; Owner: -
|
|
5624 | 5624 |
-- |
5625 | 5625 |
|
5626 |
ALTER TABLE ONLY collectiveobservation
|
|
5627 |
ADD CONSTRAINT r1collectiveobservation_taxonoccurrence_id FOREIGN KEY (taxonoccurrence_id) REFERENCES taxonoccurrence(taxonoccurrence_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
5626 |
ALTER TABLE ONLY classcontributor
|
|
5627 |
ADD CONSTRAINT r1classcontributor_commclass_id FOREIGN KEY (commclass_id) REFERENCES commclass(commclass_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
5628 | 5628 |
|
5629 | 5629 |
|
5630 | 5630 |
-- |
... | ... | |
5740 | 5740 |
|
5741 | 5741 |
|
5742 | 5742 |
-- |
5743 |
-- Name: r1individualplant_collectiveobservation_id; Type: FK CONSTRAINT; Schema: public; Owner: -
|
|
5743 |
-- Name: r1individualplant_aggregateoccurrence_id; Type: FK CONSTRAINT; Schema: public; Owner: -
|
|
5744 | 5744 |
-- |
5745 | 5745 |
|
5746 | 5746 |
ALTER TABLE ONLY individualplant |
5747 |
ADD CONSTRAINT r1individualplant_collectiveobservation_id FOREIGN KEY (collectiveobservation_id) REFERENCES collectiveobservation(collectiveobservation_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
5747 |
ADD CONSTRAINT r1individualplant_aggregateoccurrence_id FOREIGN KEY (aggregateoccurrence_id) REFERENCES aggregateoccurrence(aggregateoccurrence_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
5748 | 5748 |
|
5749 | 5749 |
|
5750 | 5750 |
-- |
... | ... | |
6092 | 6092 |
|
6093 | 6093 |
|
6094 | 6094 |
-- |
6095 |
-- Name: r2classcontributor_party_id; Type: FK CONSTRAINT; Schema: public; Owner: -
|
|
6095 |
-- Name: r2aggregateoccurrence_taxonbin_id; Type: FK CONSTRAINT; Schema: public; Owner: -
|
|
6096 | 6096 |
-- |
6097 | 6097 |
|
6098 |
ALTER TABLE ONLY classcontributor
|
|
6099 |
ADD CONSTRAINT r2classcontributor_party_id FOREIGN KEY (party_id) REFERENCES party(party_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
6098 |
ALTER TABLE ONLY aggregateoccurrence
|
|
6099 |
ADD CONSTRAINT r2aggregateoccurrence_taxonbin_id FOREIGN KEY (taxonbin_id) REFERENCES taxonbin(taxonbin_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
6100 | 6100 |
|
6101 | 6101 |
|
6102 | 6102 |
-- |
6103 |
-- Name: r2collectiveobservation_taxonbin_id; Type: FK CONSTRAINT; Schema: public; Owner: -
|
|
6103 |
-- Name: r2classcontributor_party_id; Type: FK CONSTRAINT; Schema: public; Owner: -
|
|
6104 | 6104 |
-- |
6105 | 6105 |
|
6106 |
ALTER TABLE ONLY collectiveobservation
|
|
6107 |
ADD CONSTRAINT r2collectiveobservation_taxonbin_id FOREIGN KEY (taxonbin_id) REFERENCES taxonbin(taxonbin_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
6106 |
ALTER TABLE ONLY classcontributor
|
|
6107 |
ADD CONSTRAINT r2classcontributor_party_id FOREIGN KEY (party_id) REFERENCES party(party_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
6108 | 6108 |
|
6109 | 6109 |
|
6110 | 6110 |
-- |
mappings/SALVIAS_db-VegBIEN.organisms.csv | ||
---|---|---|
1 | 1 |
SALVIAS:plotObservations,VegBIEN:/taxonoccurrence,Comments |
2 | 2 |
PlotID,/*_id/plotevent/authorcode/_alt/1,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above." |
3 | 3 |
PlotCode,"/*_id/plotevent/{*_id/plot:[confidentialitystatus=0]/authorcode/_alt/2,authorcode/_alt/2}","Brad: Same as plotCode, above" |
4 |
NoInd,/collectiveobservation/count/_alt/1,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."
|
|
5 |
cover_percent,/collectiveobservation/cover,
|
|
6 |
intercept_cm,"/collectiveobservation/definedvalue[*_id/userdefined[tablename=collectiveobservation,userdefinedname=interceptCm]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
|
|
7 |
temp_dbh,/collectiveobservation/individualplant/stemdiameter,
|
|
8 |
height_m,/collectiveobservation/individualplant/stemheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
|
|
9 |
tag2,/collectiveobservation/individualplant/stemobservation/authorcode/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
|
|
10 |
tag1,/collectiveobservation/individualplant/stemobservation/authorcode/_alt/2,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
|
|
11 |
ht_first_branch_m,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=heightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
|
|
12 |
x_position,/collectiveobservation/individualplant/stemobservation/stemxposition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX."
|
|
13 |
y_position,/collectiveobservation/individualplant/stemobservation/stemyposition,Brad: See comment above for x_position
|
|
4 |
NoInd,/aggregateoccurrence/count/_alt/1,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."
|
|
5 |
cover_percent,/aggregateoccurrence/cover,
|
|
6 |
intercept_cm,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
|
|
7 |
temp_dbh,/aggregateoccurrence/individualplant/stemdiameter,
|
|
8 |
height_m,/aggregateoccurrence/individualplant/stemheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
|
|
9 |
tag2,/aggregateoccurrence/individualplant/stemobservation/authorcode/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
|
|
10 |
tag1,/aggregateoccurrence/individualplant/stemobservation/authorcode/_alt/2,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
|
|
11 |
ht_first_branch_m,"/aggregateoccurrence/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=heightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
|
|
12 |
x_position,/aggregateoccurrence/individualplant/stemobservation/stemxposition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX."
|
|
13 |
y_position,/aggregateoccurrence/individualplant/stemobservation/stemyposition,Brad: See comment above for x_position
|
|
14 | 14 |
census_date,/taxondetermination[role_id/aux_role/rolecode=collector]/collectiondate/_date/date, |
15 | 15 |
coll_number,/taxondetermination[role_id/aux_role/rolecode=collector]/collectionnumber,Brad: Incorrect. Map instead as for voucher_string |
16 | 16 |
coll_firstname,"/taxondetermination[role_id/aux_role/rolecode=collector]/collector_id/party/{givenname/_namePart/first,middlename/_namePart/last}",Brad: See comment above |
... | ... | |
29 | 29 |
infra_ep_1,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=""Computer (automated)"",originaldetermination=false,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname/_name/last,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname/_name/last}", |
30 | 30 |
OrigFamily,"/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}",Brad: OMIT |
31 | 31 |
OrigSpecies,"/{taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname},taxondetermination[role_id/aux_role/rolecode=collector]/*_id/*/plantname/_alt/2}",Brad: OMIT |
32 |
PlotObsID,":[collectiveobservation/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/museumaccessionnumber,*_id/plotevent/authorcode/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/authorcode/_alt/3}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
|
32 |
PlotObsID,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/museumaccessionnumber,*_id/plotevent/authorcode/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/authorcode/_alt/3}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
mappings/VegX-VegBIEN.organisms.csv | ||
---|---|---|
50 | 50 |
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/maximumDepthInMeters,/*_id/plotevent/waterdepth/max |
51 | 51 |
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/minimumDepthInMeters,/*_id/plotevent/waterdepth/min |
52 | 52 |
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier,"/*_id/plotevent/{*_id/plot:[confidentialitystatus=0]/authorcode/_alt/2,authorcode/_alt/2}" |
53 |
/simpleUserdefined[name=count]/value,/collectiveobservation/count/_alt/1
|
|
54 |
/simpleUserdefined[name=coverPercent]/value,/collectiveobservation/cover
|
|
55 |
/simpleUserdefined[name=interceptCm]/value,"/collectiveobservation/definedvalue[*_id/userdefined[tablename=collectiveobservation,userdefinedname=interceptCm]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
56 |
/diameterBaseDistance[baseDistance=1.37]/diameter,/collectiveobservation/individualplant/stemdiameter
|
|
57 |
/height,/collectiveobservation/individualplant/stemheight
|
|
58 |
/simpleUserdefined[name=stemHeightM]/value,/collectiveobservation/individualplant/stemheight
|
|
59 |
/*ID->/*s/individualOrganism/identificationLabel,/collectiveobservation/individualplant/stemobservation/authorcode
|
|
60 |
/*ID->/*s/individualOrganism/identificationLabel/_alt/1,/collectiveobservation/individualplant/stemobservation/authorcode/_alt/1
|
|
61 |
/*ID->/*s/individualOrganism/identificationLabel/_alt/2,/collectiveobservation/individualplant/stemobservation/authorcode/_alt/2
|
|
62 |
/simpleUserdefined[name=habitat]/value,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=habitat]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
63 |
/simpleUserdefined[name=htFirstBranchM]/value,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=heightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
64 |
/simpleUserdefined[name=plantFungusDescription]/value,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=plantFungusDescription]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
65 |
/diameterBaseDistance[baseDistance=0]/diameter,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemBasalDiameter]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
66 |
/simpleUserdefined[name=stemCanopyForm]/value,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemCanopyForm]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
67 |
/simpleUserdefined[name=stemCanopyPosition]/value,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemCanopyPosition]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
68 |
/simpleUserdefined[name=stemHeightFirstBranchM]/value,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemHeightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
69 |
/simpleUserdefined[name=stemLianaInfestation]/value,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemLianaInfestation]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
70 |
/simpleUserdefined[name=substrate]/value,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=substrate]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
71 |
/simpleUserdefined[name=vegetation]/value,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=vegetation]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
72 |
/simpleUserdefined[name=xPosition]/value,/collectiveobservation/individualplant/stemobservation/stemxposition
|
|
73 |
/simpleUserdefined[name=yPosition]/value,/collectiveobservation/individualplant/stemobservation/stemyposition
|
|
53 |
/simpleUserdefined[name=count]/value,/aggregateoccurrence/count/_alt/1
|
|
54 |
/simpleUserdefined[name=coverPercent]/value,/aggregateoccurrence/cover
|
|
55 |
/simpleUserdefined[name=interceptCm]/value,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
56 |
/diameterBaseDistance[baseDistance=1.37]/diameter,/aggregateoccurrence/individualplant/stemdiameter
|
|
57 |
/height,/aggregateoccurrence/individualplant/stemheight
|
|
58 |
/simpleUserdefined[name=stemHeightM]/value,/aggregateoccurrence/individualplant/stemheight
|
|
59 |
/*ID->/*s/individualOrganism/identificationLabel,/aggregateoccurrence/individualplant/stemobservation/authorcode
|
|
60 |
/*ID->/*s/individualOrganism/identificationLabel/_alt/1,/aggregateoccurrence/individualplant/stemobservation/authorcode/_alt/1
|
|
61 |
/*ID->/*s/individualOrganism/identificationLabel/_alt/2,/aggregateoccurrence/individualplant/stemobservation/authorcode/_alt/2
|
|
62 |
/simpleUserdefined[name=habitat]/value,"/aggregateoccurrence/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=habitat]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
63 |
/simpleUserdefined[name=htFirstBranchM]/value,"/aggregateoccurrence/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=heightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
64 |
/simpleUserdefined[name=plantFungusDescription]/value,"/aggregateoccurrence/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=plantFungusDescription]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
65 |
/diameterBaseDistance[baseDistance=0]/diameter,"/aggregateoccurrence/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemBasalDiameter]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
66 |
/simpleUserdefined[name=stemCanopyForm]/value,"/aggregateoccurrence/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemCanopyForm]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
67 |
/simpleUserdefined[name=stemCanopyPosition]/value,"/aggregateoccurrence/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemCanopyPosition]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
68 |
/simpleUserdefined[name=stemHeightFirstBranchM]/value,"/aggregateoccurrence/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemHeightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
69 |
/simpleUserdefined[name=stemLianaInfestation]/value,"/aggregateoccurrence/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemLianaInfestation]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
70 |
/simpleUserdefined[name=substrate]/value,"/aggregateoccurrence/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=substrate]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
71 |
/simpleUserdefined[name=vegetation]/value,"/aggregateoccurrence/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=vegetation]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue"
|
|
72 |
/simpleUserdefined[name=xPosition]/value,/aggregateoccurrence/individualplant/stemobservation/stemxposition
|
|
73 |
/simpleUserdefined[name=yPosition]/value,/aggregateoccurrence/individualplant/stemobservation/stemyposition
|
|
74 | 74 |
/simpleUserdefined[name=collectionDate]/value,/taxondetermination[role_id/aux_role/rolecode=collector]/collectiondate |
75 | 75 |
/simpleUserdefined[name=collectionDate]/value/_date/date,/taxondetermination[role_id/aux_role/rolecode=collector]/collectiondate/_date/date |
76 | 76 |
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/authorCode,/taxondetermination[role_id/aux_role/rolecode=collector]/collectionnumber |
... | ... | |
107 | 107 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=ssp])/Name","/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subspecies]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}" |
108 | 108 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonName)/Simple","/{taxondetermination[role_id/aux_role/rolecode=identifier,!*_id/plantconcept]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/*_id/*/plantname,taxondetermination[role_id/aux_role/rolecode=collector]/*_id/*/plantname/_alt/1}" |
109 | 109 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=sp])/Name","/{taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname},taxondetermination[role_id/aux_role/rolecode=collector]/*_id/*/plantname/_alt/2}" |
110 |
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/voucher,":[collectiveobservation/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/museumaccessionnumber,*_id/plotevent/authorcode/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/authorcode/_alt/3}" |
|
110 |
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/voucher,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/museumaccessionnumber,*_id/plotevent/authorcode/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/authorcode/_alt/3}" |
mappings/NYBG-VegBIEN.organisms.csv | ||
---|---|---|
14 | 14 |
YearCollected,/*_id/plotevent/obsstartdate/_date/year, |
15 | 15 |
MaximumDepth,/*_id/plotevent/waterdepth/max, |
16 | 16 |
MinimumDepth,/*_id/plotevent/waterdepth/min, |
17 |
Habitat,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=habitat]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?"
|
|
18 |
PlantFungusDescription,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=plantFungusDescription]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect mapping to VB, also possibly to VX; this is the specimenDescription field, as used by this institution (NOT a standard DwC element). Very important! Bob, Nick, where would this go in VB and VX?"
|
|
19 |
Substrate,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=substrate]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect mapping to VB and VX; refers to geological substrate or soils where specimen collected. Often concatenated with habitat, or included with specimen description. Bob, Nick, is there an element for this in VB/VX, or shall we just use userDefined?"
|
|
20 |
Vegetation,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=vegetation]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Habitat'. Bob, Nick: keep as user defined or create special element?"
|
|
17 |
Habitat,"/aggregateoccurrence/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=habitat]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?"
|
|
18 |
PlantFungusDescription,"/aggregateoccurrence/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=plantFungusDescription]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect mapping to VB, also possibly to VX; this is the specimenDescription field, as used by this institution (NOT a standard DwC element). Very important! Bob, Nick, where would this go in VB and VX?"
|
|
19 |
Substrate,"/aggregateoccurrence/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=substrate]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect mapping to VB and VX; refers to geological substrate or soils where specimen collected. Often concatenated with habitat, or included with specimen description. Bob, Nick, is there an element for this in VB/VX, or shall we just use userDefined?"
|
|
20 |
Vegetation,"/aggregateoccurrence/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=vegetation]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Habitat'. Bob, Nick: keep as user defined or create special element?"
|
|
21 | 21 |
FieldNumber,/taxondetermination[role_id/aux_role/rolecode=collector]/collectionnumber,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?" |
22 | 22 |
Collector,"/taxondetermination[role_id/aux_role/rolecode=collector]/collector_id/party/{givenname/_namePart/first,middlename/_namePart/middle,surname/_namePart/last}",Brad: Correct for VB. Nick: is there a way to specifically identify this party as collector of a specimen? |
23 | 23 |
Sex,"/taxondetermination[role_id/aux_role/rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=sex]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections" |
... | ... | |
38 | 38 |
Subspecies,"/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subspecies]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}", |
39 | 39 |
ScientificName,"/{taxondetermination[role_id/aux_role/rolecode=identifier,!*_id/plantconcept]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/*_id/*/plantname,taxondetermination[role_id/aux_role/rolecode=collector]/*_id/*/plantname/_alt/1}","Brad: Bob, Nick, please is this mapping OK?" |
40 | 40 |
Species,"/{taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname},taxondetermination[role_id/aux_role/rolecode=collector]/*_id/*/plantname/_alt/2}", |
41 |
UniqueNYInternalRecordNumber,":[collectiveobservation/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/museumaccessionnumber,*_id/plotevent/authorcode/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/authorcode/_alt/3}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key" |
|
41 |
UniqueNYInternalRecordNumber,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/museumaccessionnumber,*_id/plotevent/authorcode/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/authorcode/_alt/3}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key" |
mappings/for_review/SALVIAS_db-VegBIEN.organisms.csv | ||
---|---|---|
1 | 1 |
SALVIAS:plotObservations,VegBIEN:/taxonoccurrence,Comments |
2 | 2 |
PlotID,//plotevent/authorcode/_alt/1,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above." |
3 | 3 |
PlotCode,"/*_id/plotevent/{*_id/plot/authorcode/_alt/2,authorcode/_alt/2}","Brad: Same as plotCode, above" |
4 |
NoInd,//collectiveobservation/count/_alt/1,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."
|
|
5 |
cover_percent,//collectiveobservation/cover,
|
|
6 |
intercept_cm,"//collectiveobservation/definedvalue[*_id/userdefined[tablename=collectiveobservation,userdefinedname=interceptCm]]/definedvalue","Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
|
|
4 |
NoInd,//aggregateoccurrence/count/_alt/1,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."
|
|
5 |
cover_percent,//aggregateoccurrence/cover,
|
|
6 |
intercept_cm,"//aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]]/definedvalue","Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
|
|
7 | 7 |
temp_dbh,//individualplant/stemdiameter, |
8 | 8 |
height_m,//individualplant/stemheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
9 | 9 |
tag2,//stemobservation/authorcode/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other." |
mappings/for_review/VegX-VegBIEN.organisms.csv | ||
---|---|---|
50 | 50 |
//geospatial/maximumDepthInMeters,//waterdepth/max |
51 | 51 |
//geospatial/minimumDepthInMeters,//waterdepth/min |
52 | 52 |
//plot/plotUniqueIdentifier,"/*_id/plotevent/{*_id/plot/authorcode/_alt/2,authorcode/_alt/2}" |
53 |
/simpleUserdefined[name=count]/value,//collectiveobservation/count/_alt/1
|
|
54 |
/simpleUserdefined[name=coverPercent]/value,//collectiveobservation/cover
|
|
55 |
/simpleUserdefined[name=interceptCm]/value,"//collectiveobservation/definedvalue[*_id/userdefined[tablename=collectiveobservation,userdefinedname=interceptCm]]/definedvalue"
|
|
53 |
/simpleUserdefined[name=count]/value,//aggregateoccurrence/count/_alt/1
|
|
54 |
/simpleUserdefined[name=coverPercent]/value,//aggregateoccurrence/cover
|
|
55 |
/simpleUserdefined[name=interceptCm]/value,"//aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]]/definedvalue"
|
|
56 | 56 |
/diameterBaseDistance[baseDistance=1.37]/diameter,//individualplant/stemdiameter |
57 | 57 |
/height,//individualplant/stemheight |
58 | 58 |
/simpleUserdefined[name=stemHeightM]/value,//individualplant/stemheight |
mappings/for_review/SALVIAS-VegBIEN.organisms.csv | ||
---|---|---|
2 | 2 |
plot_code,//plot/authorcode/_alt/1,"Brad: Same as plotCode, above" |
3 | 3 |
census_date,//plotevent/obsstartdate/_date/year, |
4 | 4 |
subplot,"/*_id/plotevent/{*_id/plot/authorcode/_alt/2,authorcode/_alt/2}", |
5 |
no_of_individuals,//collectiveobservation/count/_alt/1,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."
|
|
6 |
cover_percent,//collectiveobservation/cover,
|
|
7 |
intercept_cm,"//collectiveobservation/definedvalue[*_id/userdefined[tablename=collectiveobservation,userdefinedname=interceptCm]]/definedvalue","Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
|
|
5 |
no_of_individuals,//aggregateoccurrence/count/_alt/1,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."
|
|
6 |
cover_percent,//aggregateoccurrence/cover,
|
|
7 |
intercept_cm,"//aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]]/definedvalue","Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
|
|
8 | 8 |
stem_dbh,//individualplant/stemdiameter, |
9 | 9 |
height_m,//individualplant/stemheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
10 | 10 |
stem_height_m,//individualplant/stemheight,"Brad: Same as for height, but applies to individuals stems, not trees. Rare." |
mappings/SALVIAS-VegBIEN.organisms.csv | ||
---|---|---|
2 | 2 |
plot_code,/*_id/plotevent/*_id/plot/parent_id/plot:[confidentialitystatus=0]/authorcode/_alt/1,"Brad: Same as plotCode, above" |
3 | 3 |
census_date,/*_id/plotevent/obsstartdate/_date/year, |
4 | 4 |
subplot,"/*_id/plotevent/{*_id/plot:[confidentialitystatus=0]/authorcode/_alt/2,authorcode/_alt/2}", |
5 |
no_of_individuals,/collectiveobservation/count/_alt/1,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."
|
|
6 |
cover_percent,/collectiveobservation/cover,
|
|
7 |
intercept_cm,"/collectiveobservation/definedvalue[*_id/userdefined[tablename=collectiveobservation,userdefinedname=interceptCm]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
|
|
8 |
stem_dbh,/collectiveobservation/individualplant/stemdiameter,
|
|
9 |
height_m,/collectiveobservation/individualplant/stemheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
|
|
10 |
stem_height_m,/collectiveobservation/individualplant/stemheight,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
|
|
11 |
stem_tag1,/collectiveobservation/individualplant/stemobservation/authorcode,"Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems."
|
|
12 |
stem_tag2,/collectiveobservation/individualplant/stemobservation/authorcode,Brad: see above
|
|
13 |
tag2,/collectiveobservation/individualplant/stemobservation/authorcode/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
|
|
14 |
tag1,/collectiveobservation/individualplant/stemobservation/authorcode/_alt/2,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
|
|
15 |
ht_first_branch_m,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=heightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
|
|
16 |
basal_diam,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemBasalDiameter]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",
|
|
17 |
stem_canopy_form,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemCanopyForm]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Should also be userDefined for VegBank.
|
|
18 |
stem_canopy_position,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemCanopyPosition]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Should also be userDefined for VegBank.
|
|
19 |
stem_height_first_branch_m,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemHeightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."
|
|
20 |
stem_liana_infestation,"/collectiveobservation/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemLianaInfestation]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Should also be userDefined for VegBank.
|
|
21 |
x_position,/collectiveobservation/individualplant/stemobservation/stemxposition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX."
|
|
22 |
y_position,/collectiveobservation/individualplant/stemobservation/stemyposition,Brad: See comment above for x_position
|
|
5 |
no_of_individuals,/aggregateoccurrence/count/_alt/1,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."
|
|
6 |
cover_percent,/aggregateoccurrence/cover,
|
|
7 |
intercept_cm,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
|
|
8 |
stem_dbh,/aggregateoccurrence/individualplant/stemdiameter,
|
|
9 |
height_m,/aggregateoccurrence/individualplant/stemheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
|
|
10 |
stem_height_m,/aggregateoccurrence/individualplant/stemheight,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
|
|
11 |
stem_tag1,/aggregateoccurrence/individualplant/stemobservation/authorcode,"Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems."
|
|
12 |
stem_tag2,/aggregateoccurrence/individualplant/stemobservation/authorcode,Brad: see above
|
|
13 |
tag2,/aggregateoccurrence/individualplant/stemobservation/authorcode/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
|
|
14 |
tag1,/aggregateoccurrence/individualplant/stemobservation/authorcode/_alt/2,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
|
|
15 |
ht_first_branch_m,"/aggregateoccurrence/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=heightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
|
|
16 |
basal_diam,"/aggregateoccurrence/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemBasalDiameter]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",
|
|
17 |
stem_canopy_form,"/aggregateoccurrence/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemCanopyForm]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Should also be userDefined for VegBank.
|
|
18 |
stem_canopy_position,"/aggregateoccurrence/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemCanopyPosition]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Should also be userDefined for VegBank.
|
|
19 |
stem_height_first_branch_m,"/aggregateoccurrence/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemHeightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."
|
|
20 |
stem_liana_infestation,"/aggregateoccurrence/individualplant/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemLianaInfestation]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Should also be userDefined for VegBank.
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21 |
x_position,/aggregateoccurrence/individualplant/stemobservation/stemxposition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX."
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22 |
y_position,/aggregateoccurrence/individualplant/stemobservation/stemyposition,Brad: See comment above for x_position
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23 | 23 |
coll_number,/taxondetermination[role_id/aux_role/rolecode=collector]/collectionnumber,Brad: Incorrect. Map instead as for voucher_string |
24 | 24 |
coll_firstname,"/taxondetermination[role_id/aux_role/rolecode=collector]/collector_id/party/{givenname/_namePart/first,middlename/_namePart/last}",Brad: See comment above |
25 | 25 |
coll_lastname,/taxondetermination[role_id/aux_role/rolecode=collector]/collector_id/party/{surname},"Brad: Correct for VegBank. This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick." |
... | ... | |
37 | 37 |
infra_ep_1,"/taxondetermination[role_id/aux_role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=""Computer (automated)"",originaldetermination=false,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname/_name/last,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname/_name/last}", |
38 | 38 |
orig_family,"/taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname}",Brad: OMIT |
39 | 39 |
orig_species,"/{taxondetermination[role_id/aux_role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Species]:[determinationtype=Author,originaldetermination=true,currentdetermination=true,determinationdate=epoch,*_id/party]/{*_id/*/plantname,*_id/plantconcept:[plantstatus:[plantconceptstatus=accepted,startdate=epoch,*_id/party],*_id/reference]/*_id/*/plantname},taxondetermination[role_id/aux_role/rolecode=collector]/*_id/*/plantname/_alt/2}",Brad: OMIT |
40 |
OBSERVATION_ID,":[collectiveobservation/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/museumaccessionnumber,*_id/plotevent/authorcode/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/authorcode/_alt/3}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
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40 |
OBSERVATION_ID,":[aggregateoccurrence/count/_alt/2=1]/{taxondetermination[role_id/aux_role/rolecode=collector]:[determinationtype=Author,originaldetermination=true,currentdetermination=false,determinationdate=epoch,*_id/party]/museumaccessionnumber,*_id/plotevent/authorcode/_alt/2,*_id/plotevent/*_id/plot:[confidentialitystatus=0]/authorcode/_alt/3}","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
Also available in: Unified diff
VegBIEN: Renamed collectiveobservation to aggregateoccurrence to reflect VegX usage of aggregate and the new taxonoccurrence table