Revision 489
Added by Aaron Marcuse-Kubitza almost 13 years ago
| test/accepted_output/SALVIAS.organisms.VegBIEN.xml | ||
|---|---|---|
| 22 | 22 |
<aggregateoccurrence> |
| 23 | 23 |
<count>1</count> |
| 24 | 24 |
<individualplant> |
| 25 |
<stem> |
|
| 26 |
<authorcode>8</authorcode> |
|
| 27 |
</stem> |
|
| 25 | 28 |
<stemdiameter>662</stemdiameter> |
| 26 |
<stemobservation> |
|
| 27 |
<authorcode>8</authorcode> |
|
| 28 |
</stemobservation> |
|
| 29 | 29 |
</individualplant> |
| 30 | 30 |
</aggregateoccurrence> |
| 31 | 31 |
<taxondetermination> |
| ... | ... | |
| 302 | 302 |
<aggregateoccurrence> |
| 303 | 303 |
<count>1</count> |
| 304 | 304 |
<individualplant> |
| 305 |
<stem> |
|
| 306 |
<authorcode>91</authorcode> |
|
| 307 |
</stem> |
|
| 305 | 308 |
<stemdiameter>215</stemdiameter> |
| 306 |
<stemobservation> |
|
| 307 |
<authorcode>91</authorcode> |
|
| 308 |
</stemobservation> |
|
| 309 | 309 |
</individualplant> |
| 310 | 310 |
</aggregateoccurrence> |
| 311 | 311 |
<taxondetermination> |
| test/accepted_output/NYBG.organisms.VegBIEN.xml | ||
|---|---|---|
| 44 | 44 |
</plotevent_id> |
| 45 | 45 |
<aggregateoccurrence> |
| 46 | 46 |
<individualplant> |
| 47 |
<stemobservation>
|
|
| 47 |
<stem> |
|
| 48 | 48 |
<definedvalue fkey="tableRecord_ID"> |
| 49 | 49 |
<userdefined_id> |
| 50 | 50 |
<userdefined> |
| 51 |
<tablename>stemobservation</tablename>
|
|
| 51 |
<tablename>stem</tablename> |
|
| 52 | 52 |
<userdefinedname>habitat</userdefinedname> |
| 53 | 53 |
<userdefinedtype>varchar</userdefinedtype> |
| 54 | 54 |
</userdefined> |
| ... | ... | |
| 58 | 58 |
<definedvalue fkey="tableRecord_ID"> |
| 59 | 59 |
<userdefined_id> |
| 60 | 60 |
<userdefined> |
| 61 |
<tablename>stemobservation</tablename>
|
|
| 61 |
<tablename>stem</tablename> |
|
| 62 | 62 |
<userdefinedname>plantFungusDescription</userdefinedname> |
| 63 | 63 |
<userdefinedtype>varchar</userdefinedtype> |
| 64 | 64 |
</userdefined> |
| 65 | 65 |
</userdefined_id> |
| 66 | 66 |
<definedvalue>with rough brown bark, almost no buttressing, 1 m diam; fallen fruit and leaves</definedvalue> |
| 67 | 67 |
</definedvalue> |
| 68 |
</stemobservation>
|
|
| 68 |
</stem> |
|
| 69 | 69 |
</individualplant> |
| 70 | 70 |
<count>1</count> |
| 71 | 71 |
</aggregateoccurrence> |
| inputs/SALVIAS/map.VegBIEN.organisms.csv | ||
|---|---|---|
| 4 | 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 | 5 |
cover_percent,/aggregateoccurrence/cover, |
| 6 | 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 |
tag2,/aggregateoccurrence/individualplant/stem/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." |
|
| 8 |
tag1,/aggregateoccurrence/individualplant/stem/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." |
|
| 9 |
ht_first_branch_m,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
|
| 10 |
x_position,/aggregateoccurrence/individualplant/stem/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." |
|
| 11 |
y_position,/aggregateoccurrence/individualplant/stem/stemyposition,Brad: See comment above for x_position |
|
| 7 | 12 |
temp_dbh,/aggregateoccurrence/individualplant/stemdiameter, |
| 8 | 13 |
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
|
| schemas/vegbien_empty.sql | ||
|---|---|---|
| 60 | 60 |
TRUNCATE soilobs CASCADE; |
| 61 | 61 |
TRUNCATE soiltaxon CASCADE; |
| 62 | 62 |
TRUNCATE specimen CASCADE; |
| 63 |
TRUNCATE stemobservation CASCADE;
|
|
| 63 |
TRUNCATE stem CASCADE; |
|
| 64 | 64 |
TRUNCATE stratum CASCADE; |
| 65 | 65 |
TRUNCATE stratummethod CASCADE; |
| 66 | 66 |
TRUNCATE stratumtype CASCADE; |
| schemas/vegbien.sql | ||
|---|---|---|
| 1655 | 1655 |
methodnarrative text, |
| 1656 | 1656 |
taxonoccurrencearea double precision, |
| 1657 | 1657 |
stemsizelimit double precision, |
| 1658 |
stemobservationarea double precision,
|
|
| 1658 |
stemarea double precision, |
|
| 1659 | 1659 |
stemsamplemethod character varying(30), |
| 1660 | 1660 |
originaldata text, |
| 1661 | 1661 |
effortlevel character varying(30), |
| ... | ... | |
| 2287 | 2287 |
SET default_with_oids = true; |
| 2288 | 2288 |
|
| 2289 | 2289 |
-- |
| 2290 |
-- Name: stemobservation; Type: TABLE; Schema: public; Owner: -; Tablespace:
|
|
| 2290 |
-- Name: stem; Type: TABLE; Schema: public; Owner: -; Tablespace: |
|
| 2291 | 2291 |
-- |
| 2292 | 2292 |
|
| 2293 |
CREATE TABLE stemobservation (
|
|
| 2294 |
stemobservation_id integer NOT NULL,
|
|
| 2293 |
CREATE TABLE stem ( |
|
| 2294 |
stem_id integer NOT NULL, |
|
| 2295 | 2295 |
individualplant_id integer NOT NULL, |
| 2296 | 2296 |
authorcode character varying(20), |
| 2297 | 2297 |
stemxposition double precision, |
| 2298 | 2298 |
stemyposition double precision, |
| 2299 | 2299 |
stemhealth character varying(50), |
| 2300 |
emb_stemobservation integer,
|
|
| 2300 |
emb_stem integer, |
|
| 2301 | 2301 |
stemdiameter double precision, |
| 2302 | 2302 |
stemheight double precision, |
| 2303 | 2303 |
stemheightaccuracy double precision, |
| ... | ... | |
| 2306 | 2306 |
|
| 2307 | 2307 |
|
| 2308 | 2308 |
-- |
| 2309 |
-- Name: TABLE stemobservation; Type: COMMENT; Schema: public; Owner: -
|
|
| 2309 |
-- Name: TABLE stem; Type: COMMENT; Schema: public; Owner: - |
|
| 2310 | 2310 |
-- |
| 2311 | 2311 |
|
| 2312 |
COMMENT ON TABLE stemobservation IS 'VegBank''s stemlocation table.';
|
|
| 2312 |
COMMENT ON TABLE stem IS 'VegBank''s stemlocation table.'; |
|
| 2313 | 2313 |
|
| 2314 | 2314 |
|
| 2315 | 2315 |
-- |
| 2316 |
-- Name: stemobservation_stemobservation_id_seq; Type: SEQUENCE; Schema: public; Owner: -
|
|
| 2316 |
-- Name: stem_stem_id_seq; Type: SEQUENCE; Schema: public; Owner: -
|
|
| 2317 | 2317 |
-- |
| 2318 | 2318 |
|
| 2319 |
CREATE SEQUENCE stemobservation_stemobservation_id_seq
|
|
| 2319 |
CREATE SEQUENCE stem_stem_id_seq
|
|
| 2320 | 2320 |
START WITH 1 |
| 2321 | 2321 |
INCREMENT BY 1 |
| 2322 | 2322 |
NO MINVALUE |
| ... | ... | |
| 2325 | 2325 |
|
| 2326 | 2326 |
|
| 2327 | 2327 |
-- |
| 2328 |
-- Name: stemobservation_stemobservation_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
|
|
| 2328 |
-- Name: stem_stem_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
|
|
| 2329 | 2329 |
-- |
| 2330 | 2330 |
|
| 2331 |
ALTER SEQUENCE stemobservation_stemobservation_id_seq OWNED BY stemobservation.stemobservation_id;
|
|
| 2331 |
ALTER SEQUENCE stem_stem_id_seq OWNED BY stem.stem_id;
|
|
| 2332 | 2332 |
|
| 2333 | 2333 |
|
| 2334 | 2334 |
-- |
| ... | ... | |
| 2493 | 2493 |
CREATE TABLE taxondetermination ( |
| 2494 | 2494 |
taxondetermination_id integer NOT NULL, |
| 2495 | 2495 |
taxonoccurrence_id integer NOT NULL, |
| 2496 |
stemobservation_id integer,
|
|
| 2496 |
stem_id integer, |
|
| 2497 | 2497 |
plantconcept_id integer, |
| 2498 | 2498 |
plantname_id integer NOT NULL, |
| 2499 | 2499 |
party_id integer NOT NULL, |
| ... | ... | |
| 2702 | 2702 |
|
| 2703 | 2703 |
CREATE TABLE trait ( |
| 2704 | 2704 |
trait_id integer NOT NULL, |
| 2705 |
stemobservation_id integer NOT NULL,
|
|
| 2705 |
stem_id integer NOT NULL, |
|
| 2706 | 2706 |
type character varying(255) NOT NULL, |
| 2707 | 2707 |
value character varying(255) |
| 2708 | 2708 |
); |
| ... | ... | |
| 3556 | 3556 |
|
| 3557 | 3557 |
|
| 3558 | 3558 |
-- |
| 3559 |
-- Name: stemobservation_id; Type: DEFAULT; Schema: public; Owner: -
|
|
| 3559 |
-- Name: stem_id; Type: DEFAULT; Schema: public; Owner: - |
|
| 3560 | 3560 |
-- |
| 3561 | 3561 |
|
| 3562 |
ALTER TABLE stemobservation ALTER COLUMN stemobservation_id SET DEFAULT nextval('stemobservation_stemobservation_id_seq'::regclass);
|
|
| 3562 |
ALTER TABLE stem ALTER COLUMN stem_id SET DEFAULT nextval('stem_stem_id_seq'::regclass);
|
|
| 3563 | 3563 |
|
| 3564 | 3564 |
|
| 3565 | 3565 |
-- |
| ... | ... | |
| 4294 | 4294 |
|
| 4295 | 4295 |
|
| 4296 | 4296 |
-- |
| 4297 |
-- Name: stemobservation_keys; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
|
|
| 4297 |
-- Name: stem_keys; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace: |
|
| 4298 | 4298 |
-- |
| 4299 | 4299 |
|
| 4300 |
ALTER TABLE ONLY stemobservation
|
|
| 4301 |
ADD CONSTRAINT stemobservation_keys UNIQUE (individualplant_id, authorcode);
|
|
| 4300 |
ALTER TABLE ONLY stem |
|
| 4301 |
ADD CONSTRAINT stem_keys UNIQUE (individualplant_id, authorcode); |
|
| 4302 | 4302 |
|
| 4303 | 4303 |
|
| 4304 | 4304 |
-- |
| 4305 |
-- Name: stemobservation_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
|
|
| 4305 |
-- Name: stem_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace: |
|
| 4306 | 4306 |
-- |
| 4307 | 4307 |
|
| 4308 |
ALTER TABLE ONLY stemobservation
|
|
| 4309 |
ADD CONSTRAINT stemobservation_pkey PRIMARY KEY (stemobservation_id);
|
|
| 4308 |
ALTER TABLE ONLY stem |
|
| 4309 |
ADD CONSTRAINT stem_pkey PRIMARY KEY (stem_id);
|
|
| 4310 | 4310 |
|
| 4311 | 4311 |
|
| 4312 | 4312 |
-- |
| ... | ... | |
| 4354 | 4354 |
-- |
| 4355 | 4355 |
|
| 4356 | 4356 |
ALTER TABLE ONLY taxondetermination |
| 4357 |
ADD CONSTRAINT taxondetermination_keys UNIQUE (taxonoccurrence_id, stemobservation_id, role_id, plantname_id, museumaccessionnumber);
|
|
| 4357 |
ADD CONSTRAINT taxondetermination_keys UNIQUE (taxonoccurrence_id, stem_id, role_id, plantname_id, museumaccessionnumber); |
|
| 4358 | 4358 |
|
| 4359 | 4359 |
|
| 4360 | 4360 |
-- |
| ... | ... | |
| 4852 | 4852 |
|
| 4853 | 4853 |
|
| 4854 | 4854 |
-- |
| 4855 |
-- Name: emb_stemobservation_idx; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
| 4855 |
-- Name: emb_stem_idx; Type: INDEX; Schema: public; Owner: -; Tablespace: |
|
| 4856 | 4856 |
-- |
| 4857 | 4857 |
|
| 4858 |
CREATE INDEX emb_stemobservation_idx ON stemobservation USING btree (emb_stemobservation);
|
|
| 4858 |
CREATE INDEX emb_stem_idx ON stem USING btree (emb_stem);
|
|
| 4859 | 4859 |
|
| 4860 | 4860 |
|
| 4861 | 4861 |
-- |
| ... | ... | |
| 5426 | 5426 |
|
| 5427 | 5427 |
|
| 5428 | 5428 |
-- |
| 5429 |
-- Name: stemobservation_individualplant_id_x; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
| 5429 |
-- Name: stem_individualplant_id_x; Type: INDEX; Schema: public; Owner: -; Tablespace: |
|
| 5430 | 5430 |
-- |
| 5431 | 5431 |
|
| 5432 |
CREATE INDEX stemobservation_individualplant_id_x ON stemobservation USING btree (individualplant_id);
|
|
| 5432 |
CREATE INDEX stem_individualplant_id_x ON stem USING btree (individualplant_id);
|
|
| 5433 | 5433 |
|
| 5434 | 5434 |
|
| 5435 | 5435 |
-- |
| ... | ... | |
| 5545 | 5545 |
|
| 5546 | 5546 |
|
| 5547 | 5547 |
-- |
| 5548 |
-- Name: taxondetermination_stemobservation_id_x; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
| 5548 |
-- Name: taxondetermination_stem_id_x; Type: INDEX; Schema: public; Owner: -; Tablespace: |
|
| 5549 | 5549 |
-- |
| 5550 | 5550 |
|
| 5551 |
CREATE INDEX taxondetermination_stemobservation_id_x ON taxondetermination USING btree (stemobservation_id);
|
|
| 5551 |
CREATE INDEX taxondetermination_stem_id_x ON taxondetermination USING btree (stem_id);
|
|
| 5552 | 5552 |
|
| 5553 | 5553 |
|
| 5554 | 5554 |
-- |
| ... | ... | |
| 6433 | 6433 |
|
| 6434 | 6434 |
|
| 6435 | 6435 |
-- |
| 6436 |
-- Name: stemobservation_individualplant_id; Type: FK CONSTRAINT; Schema: public; Owner: -
|
|
| 6436 |
-- Name: stem_individualplant_id; Type: FK CONSTRAINT; Schema: public; Owner: - |
|
| 6437 | 6437 |
-- |
| 6438 | 6438 |
|
| 6439 |
ALTER TABLE ONLY stemobservation
|
|
| 6440 |
ADD CONSTRAINT stemobservation_individualplant_id FOREIGN KEY (individualplant_id) REFERENCES individualplant(individualplant_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
| 6439 |
ALTER TABLE ONLY stem |
|
| 6440 |
ADD CONSTRAINT stem_individualplant_id FOREIGN KEY (individualplant_id) REFERENCES individualplant(individualplant_id) ON UPDATE CASCADE ON DELETE CASCADE; |
|
| 6441 | 6441 |
|
| 6442 | 6442 |
|
| 6443 | 6443 |
-- |
| ... | ... | |
| 6569 | 6569 |
|
| 6570 | 6570 |
|
| 6571 | 6571 |
-- |
| 6572 |
-- Name: taxondetermination_stemobservation_id; Type: FK CONSTRAINT; Schema: public; Owner: -
|
|
| 6572 |
-- Name: taxondetermination_stem_id; Type: FK CONSTRAINT; Schema: public; Owner: - |
|
| 6573 | 6573 |
-- |
| 6574 | 6574 |
|
| 6575 | 6575 |
ALTER TABLE ONLY taxondetermination |
| 6576 |
ADD CONSTRAINT taxondetermination_stemobservation_id FOREIGN KEY (stemobservation_id) REFERENCES stemobservation(stemobservation_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
| 6576 |
ADD CONSTRAINT taxondetermination_stem_id FOREIGN KEY (stem_id) REFERENCES stem(stem_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
| 6577 | 6577 |
|
| 6578 | 6578 |
|
| 6579 | 6579 |
-- |
| ... | ... | |
| 6609 | 6609 |
|
| 6610 | 6610 |
|
| 6611 | 6611 |
-- |
| 6612 |
-- Name: trait_stemobservation_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: -
|
|
| 6612 |
-- Name: trait_stem_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: - |
|
| 6613 | 6613 |
-- |
| 6614 | 6614 |
|
| 6615 | 6615 |
ALTER TABLE ONLY trait |
| 6616 |
ADD CONSTRAINT trait_stemobservation_id_fkey FOREIGN KEY (stemobservation_id) REFERENCES stemobservation(stemobservation_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
| 6616 |
ADD CONSTRAINT trait_stem_id_fkey FOREIGN KEY (stem_id) REFERENCES stem(stem_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
| 6617 | 6617 |
|
| 6618 | 6618 |
|
| 6619 | 6619 |
-- |
| mappings/SALVIAS_db-VegBIEN.organisms.csv | ||
|---|---|---|
| 4 | 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 | 5 |
cover_percent,/aggregateoccurrence/cover, |
| 6 | 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 |
tag2,/aggregateoccurrence/individualplant/stem/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." |
|
| 8 |
tag1,/aggregateoccurrence/individualplant/stem/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." |
|
| 9 |
ht_first_branch_m,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
|
| 10 |
x_position,/aggregateoccurrence/individualplant/stem/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." |
|
| 11 |
y_position,/aggregateoccurrence/individualplant/stem/stemyposition,Brad: See comment above for x_position |
|
| 7 | 12 |
temp_dbh,/aggregateoccurrence/individualplant/stemdiameter, |
| 8 | 13 |
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
|
| mappings/VegX-VegBIEN.organisms.csv | ||
|---|---|---|
| 53 | 53 |
/simpleUserdefined[name=count]/value,/aggregateoccurrence/count/_alt/1 |
| 54 | 54 |
/simpleUserdefined[name=coverPercent]/value,/aggregateoccurrence/cover |
| 55 | 55 |
/simpleUserdefined[name=interceptCm]/value,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue" |
| 56 |
/*ID->/*s/individualOrganism/identificationLabel,/aggregateoccurrence/individualplant/stem/authorcode |
|
| 57 |
/*ID->/*s/individualOrganism/identificationLabel/_alt/1,/aggregateoccurrence/individualplant/stem/authorcode/_alt/1 |
|
| 58 |
/*ID->/*s/individualOrganism/identificationLabel/_alt/2,/aggregateoccurrence/individualplant/stem/authorcode/_alt/2 |
|
| 59 |
/simpleUserdefined[name=habitat]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=habitat]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue" |
|
| 60 |
/simpleUserdefined[name=htFirstBranchM]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue" |
|
| 61 |
/simpleUserdefined[name=plantFungusDescription]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=plantFungusDescription]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue" |
|
| 62 |
/diameterBaseDistance[baseDistance=0]/diameter,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemBasalDiameter]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue" |
|
| 63 |
/simpleUserdefined[name=stemCanopyForm]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemCanopyForm]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue" |
|
| 64 |
/simpleUserdefined[name=stemCanopyPosition]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemCanopyPosition]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue" |
|
| 65 |
/simpleUserdefined[name=stemHeightFirstBranchM]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemHeightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue" |
|
| 66 |
/simpleUserdefined[name=stemLianaInfestation]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemLianaInfestation]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue" |
|
| 67 |
/simpleUserdefined[name=substrate]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=substrate]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue" |
|
| 68 |
/simpleUserdefined[name=vegetation]/value,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=vegetation]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue" |
|
| 69 |
/simpleUserdefined[name=xPosition]/value,/aggregateoccurrence/individualplant/stem/stemxposition |
|
| 70 |
/simpleUserdefined[name=yPosition]/value,/aggregateoccurrence/individualplant/stem/stemyposition |
|
| 56 | 71 |
/diameterBaseDistance[baseDistance=1.37]/diameter,/aggregateoccurrence/individualplant/stemdiameter |
| 57 | 72 |
/height,/aggregateoccurrence/individualplant/stemheight |
| 58 | 73 |
/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 |
| mappings/VegBIEN-VegBank.csv | ||
|---|---|---|
| 4 | 4 |
"taxonoccurrence","taxonobservation", |
| 5 | 5 |
"aggregateoccurrence","taxonimportance", |
| 6 | 6 |
"individualplant","stemcount", |
| 7 |
"stemobservation","stemlocation",
|
|
| 7 |
"stem","stemlocation", |
|
| 8 | 8 |
"taxondetermination","taxoninterpretation", |
| 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,"/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?"
|
|
| 17 |
Habitat,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,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/stem/definedvalue[*_id/userdefined[tablename=stem,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/stem/definedvalue[*_id/userdefined[tablename=stem,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/stem/definedvalue[*_id/userdefined[tablename=stem,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" |
| mappings/for_review/SALVIAS_db-VegBIEN.organisms.csv | ||
|---|---|---|
| 4 | 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 | 5 |
cover_percent,//aggregateoccurrence/cover, |
| 6 | 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 |
tag2,//stem/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." |
|
| 8 |
tag1,//stem/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." |
|
| 9 |
ht_first_branch_m,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
|
| 10 |
x_position,//stem/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." |
|
| 11 |
y_position,//stem/stemyposition,Brad: See comment above for x_position |
|
| 7 | 12 |
temp_dbh,//individualplant/stemdiameter, |
| 8 | 13 |
height_m,//individualplant/stemheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
| 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." |
|
| 10 |
tag1,//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,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=heightFirstBranchM]]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
|
| 12 |
x_position,//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,//stemobservation/stemyposition,Brad: See comment above for x_position |
|
| 14 | 14 |
census_date,/taxondetermination[rolecode=collector]/collectiondate/_date/date, |
| 15 | 15 |
coll_number,/taxondetermination[rolecode=collector]/collectionnumber,Brad: Incorrect. Map instead as for voucher_string |
| 16 | 16 |
coll_firstname,"/taxondetermination[rolecode=collector]/collector_id/party/{givenname/_namePart/first,middlename/_namePart/last}",Brad: See comment above
|
| mappings/for_review/VegX-VegBIEN.organisms.csv | ||
|---|---|---|
| 53 | 53 |
/simpleUserdefined[name=count]/value,//aggregateoccurrence/count/_alt/1 |
| 54 | 54 |
/simpleUserdefined[name=coverPercent]/value,//aggregateoccurrence/cover |
| 55 | 55 |
/simpleUserdefined[name=interceptCm]/value,"//aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=interceptCm]]/definedvalue" |
| 56 |
//individualOrganism/identificationLabel,//stem/authorcode |
|
| 57 |
//individualOrganism/identificationLabel/_alt/1,//stem/authorcode/_alt/1 |
|
| 58 |
//individualOrganism/identificationLabel/_alt/2,//stem/authorcode/_alt/2 |
|
| 59 |
/simpleUserdefined[name=habitat]/value,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=habitat]]/definedvalue" |
|
| 60 |
/simpleUserdefined[name=htFirstBranchM]/value,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]]/definedvalue" |
|
| 61 |
/simpleUserdefined[name=plantFungusDescription]/value,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=plantFungusDescription]]/definedvalue" |
|
| 62 |
/diameterBaseDistance[baseDistance=0]/diameter,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemBasalDiameter]]/definedvalue" |
|
| 63 |
/simpleUserdefined[name=stemCanopyForm]/value,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemCanopyForm]]/definedvalue" |
|
| 64 |
/simpleUserdefined[name=stemCanopyPosition]/value,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemCanopyPosition]]/definedvalue" |
|
| 65 |
/simpleUserdefined[name=stemHeightFirstBranchM]/value,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemHeightFirstBranchM]]/definedvalue" |
|
| 66 |
/simpleUserdefined[name=stemLianaInfestation]/value,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemLianaInfestation]]/definedvalue" |
|
| 67 |
/simpleUserdefined[name=substrate]/value,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=substrate]]/definedvalue" |
|
| 68 |
/simpleUserdefined[name=vegetation]/value,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=vegetation]]/definedvalue" |
|
| 69 |
/simpleUserdefined[name=xPosition]/value,//stem/stemxposition |
|
| 70 |
/simpleUserdefined[name=yPosition]/value,//stem/stemyposition |
|
| 56 | 71 |
/diameterBaseDistance[baseDistance=1.37]/diameter,//individualplant/stemdiameter |
| 57 | 72 |
/height,//individualplant/stemheight |
| 58 | 73 |
/simpleUserdefined[name=stemHeightM]/value,//individualplant/stemheight |
| 59 |
//individualOrganism/identificationLabel,//stemobservation/authorcode |
|
| 60 |
//individualOrganism/identificationLabel/_alt/1,//stemobservation/authorcode/_alt/1 |
|
| 61 |
//individualOrganism/identificationLabel/_alt/2,//stemobservation/authorcode/_alt/2 |
|
| 62 |
/simpleUserdefined[name=habitat]/value,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=habitat]]/definedvalue" |
|
| 63 |
/simpleUserdefined[name=htFirstBranchM]/value,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=heightFirstBranchM]]/definedvalue" |
|
| 64 |
/simpleUserdefined[name=plantFungusDescription]/value,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=plantFungusDescription]]/definedvalue" |
|
| 65 |
/diameterBaseDistance[baseDistance=0]/diameter,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemBasalDiameter]]/definedvalue" |
|
| 66 |
/simpleUserdefined[name=stemCanopyForm]/value,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemCanopyForm]]/definedvalue" |
|
| 67 |
/simpleUserdefined[name=stemCanopyPosition]/value,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemCanopyPosition]]/definedvalue" |
|
| 68 |
/simpleUserdefined[name=stemHeightFirstBranchM]/value,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemHeightFirstBranchM]]/definedvalue" |
|
| 69 |
/simpleUserdefined[name=stemLianaInfestation]/value,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemLianaInfestation]]/definedvalue" |
|
| 70 |
/simpleUserdefined[name=substrate]/value,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=substrate]]/definedvalue" |
|
| 71 |
/simpleUserdefined[name=vegetation]/value,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=vegetation]]/definedvalue" |
|
| 72 |
/simpleUserdefined[name=xPosition]/value,//stemobservation/stemxposition |
|
| 73 |
/simpleUserdefined[name=yPosition]/value,//stemobservation/stemyposition |
|
| 74 | 74 |
/simpleUserdefined[name=collectionDate]/value,/taxondetermination[rolecode=collector]/collectiondate |
| 75 | 75 |
/simpleUserdefined[name=collectionDate]/value/_date/date,/taxondetermination[rolecode=collector]/collectiondate/_date/date |
| 76 | 76 |
//taxonNameUsageConcept/authorCode,/taxondetermination[rolecode=collector]/collectionnumber |
| mappings/for_review/NYBG-VegBIEN.organisms.csv | ||
|---|---|---|
| 14 | 14 |
YearCollected,//plotevent/obsstartdate/_date/year, |
| 15 | 15 |
MaximumDepth,//waterdepth/max, |
| 16 | 16 |
MinimumDepth,//waterdepth/min, |
| 17 |
Habitat,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=habitat]]/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,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=plantFungusDescription]]/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,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=substrate]]/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,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=vegetation]]/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,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=habitat]]/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,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=plantFungusDescription]]/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,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=substrate]]/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,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=vegetation]]/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[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[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[rolecode=collector]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=sex]]/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" |
| mappings/for_review/SALVIAS-VegBIEN.organisms.csv | ||
|---|---|---|
| 5 | 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 | 6 |
cover_percent,//aggregateoccurrence/cover, |
| 7 | 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 |
stem_tag1,//stem/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." |
|
| 9 |
stem_tag2,//stem/authorcode,Brad: see above |
|
| 10 |
tag2,//stem/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." |
|
| 11 |
tag1,//stem/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." |
|
| 12 |
ht_first_branch_m,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
|
| 13 |
basal_diam,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemBasalDiameter]]/definedvalue", |
|
| 14 |
stem_canopy_form,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemCanopyForm]]/definedvalue",Brad: Should also be userDefined for VegBank. |
|
| 15 |
stem_canopy_position,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemCanopyPosition]]/definedvalue",Brad: Should also be userDefined for VegBank. |
|
| 16 |
stem_height_first_branch_m,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemHeightFirstBranchM]]/definedvalue","Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare." |
|
| 17 |
stem_liana_infestation,"//stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemLianaInfestation]]/definedvalue",Brad: Should also be userDefined for VegBank. |
|
| 18 |
x_position,//stem/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." |
|
| 19 |
y_position,//stem/stemyposition,Brad: See comment above for x_position |
|
| 8 | 20 |
stem_dbh,//individualplant/stemdiameter, |
| 9 | 21 |
height_m,//individualplant/stemheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
| 10 | 22 |
stem_height_m,//individualplant/stemheight,"Brad: Same as for height, but applies to individuals stems, not trees. Rare." |
| 11 |
stem_tag1,//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,//stemobservation/authorcode,Brad: see above |
|
| 13 |
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." |
|
| 14 |
tag1,//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,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=heightFirstBranchM]]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
|
| 16 |
basal_diam,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemBasalDiameter]]/definedvalue", |
|
| 17 |
stem_canopy_form,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemCanopyForm]]/definedvalue",Brad: Should also be userDefined for VegBank. |
|
| 18 |
stem_canopy_position,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemCanopyPosition]]/definedvalue",Brad: Should also be userDefined for VegBank. |
|
| 19 |
stem_height_first_branch_m,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemHeightFirstBranchM]]/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,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=stemLianaInfestation]]/definedvalue",Brad: Should also be userDefined for VegBank. |
|
| 21 |
x_position,//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,//stemobservation/stemyposition,Brad: See comment above for x_position |
|
| 23 | 23 |
coll_number,/taxondetermination[rolecode=collector]/collectionnumber,Brad: Incorrect. Map instead as for voucher_string |
| 24 | 24 |
coll_firstname,"/taxondetermination[rolecode=collector]/collector_id/party/{givenname/_namePart/first,middlename/_namePart/last}",Brad: See comment above
|
| 25 | 25 |
coll_lastname,/taxondetermination[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."
|
| mappings/SALVIAS-VegBIEN.organisms.csv | ||
|---|---|---|
| 5 | 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 | 6 |
cover_percent,/aggregateoccurrence/cover, |
| 7 | 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_tag1,/aggregateoccurrence/individualplant/stem/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." |
|
| 9 |
stem_tag2,/aggregateoccurrence/individualplant/stem/authorcode,Brad: see above |
|
| 10 |
tag2,/aggregateoccurrence/individualplant/stem/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." |
|
| 11 |
tag1,/aggregateoccurrence/individualplant/stem/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." |
|
| 12 |
ht_first_branch_m,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=heightFirstBranchM]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
|
| 13 |
basal_diam,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemBasalDiameter]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue", |
|
| 14 |
stem_canopy_form,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemCanopyForm]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Should also be userDefined for VegBank. |
|
| 15 |
stem_canopy_position,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemCanopyPosition]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Should also be userDefined for VegBank. |
|
| 16 |
stem_height_first_branch_m,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,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." |
|
| 17 |
stem_liana_infestation,"/aggregateoccurrence/individualplant/stem/definedvalue[*_id/userdefined[tablename=stem,userdefinedname=stemLianaInfestation]:[userdefinedtype=varchar]]:[@fkey=tableRecord_ID]/definedvalue",Brad: Should also be userDefined for VegBank. |
|
| 18 |
x_position,/aggregateoccurrence/individualplant/stem/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." |
|
| 19 |
y_position,/aggregateoccurrence/individualplant/stem/stemyposition,Brad: See comment above for x_position |
|
| 8 | 20 |
stem_dbh,/aggregateoccurrence/individualplant/stemdiameter, |
| 9 | 21 |
height_m,/aggregateoccurrence/individualplant/stemheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
| 10 | 22 |
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. |
|
| 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." |
|
| 22 |
y_position,/aggregateoccurrence/individualplant/stemobservation/stemyposition,Brad: See comment above for x_position |
|
| 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."
|
Also available in: Unified diff
VegBIEN: Renamed stemobservation to stem