There are many fields that can be obtained via the Search and Media API. This tutorial is meant to aid in identifying these fields.
General Overview
In this demo we will cover how to:
- Identifying both raw and indexed record fields with
idig_meta_fields() - Downloading fields of interest with
idig_search_records() - Identifying both raw and indexed media record fields with
idig_meta_fields() - Downloading fields of interest with
idig_search_media()
Search API Fields
To identify the raw, or verbatim, fields available with the Search API, you can run the following:
record_fields <- idig_meta_fields(type = "records", subset = "raw")
rfall <- data.frame(matrix(ncol = 2, nrow = 0))
colnames(rfall) <- c("Type", "FieldNameValue")
for(i in 1:length(record_fields)) {
rf <- data.frame(
Type = record_fields[[i]]$type,
FieldNameValue = record_fields[[i]]$fieldName,
stringsAsFactors = FALSE
)
rfall <- rbind(rfall, rf)
}
colnames(rfall) <- c("type", "fieldName")
nrow(rfall)## [1] 219In addition to the fields provided by data providers, the Search API contains fields that have been indexed and potentially modified by iDigBio. To identify the indexed fields available with the Search API, you can run the following:
record_fields_index <- idig_meta_fields(type = "records", subset = "indexed")
rfalli <- data.frame(matrix(ncol = 2, nrow = 0))
colnames(rfalli) <- c("Type", "FieldNameValue")
for(i in 1:length(record_fields_index)) {
rf <- data.frame(
Type = record_fields_index[[i]]$type,
FieldNameValue = record_fields_index[[i]]$fieldName,
stringsAsFactors = FALSE
)
rfalli <- rbind(rfalli, rf)
}
colnames(rfalli) <- c("type", "fieldName")
nrow(rfalli)## [1] 82Note, these fields lists are different.
setequal(rfall, rfalli)## [1] FALSEHowever, they contain similar information. For example, scientificName can be found in both the raw and index fields.
rfall[171,]## type fieldName
## 171 string data.dwc:scientificName
rfalli[69,]## type fieldName
## 69 string scientificnameRetain records with these fields
To obtain records with these fields with the
idig_search_records() function, you simply list the
fields arugument as equal to these fields.
out <- idig_search_records(rq=list(scientificname="Galax urceolata"),
fields = rfall$fieldName)Media Record API Fields
To identify the raw, or verbatim, fields available with the Media Record API, you can run the following:
media_fields <- idig_meta_fields(type = "media", subset = "raw")
mfall <- data.frame(matrix(ncol = 2, nrow = 0))
colnames(mfall) <- c("Type", "FieldNameValue")
for(i in 1:length(media_fields)) {
mf <- data.frame(
Type = media_fields[[i]]$type,
FieldNameValue = media_fields[[i]]$fieldName,
stringsAsFactors = FALSE
)
mfall <- rbind(mfall, mf)
}
colnames(mfall) <- c("type", "fieldName")
nrow(mfall)## [1] 139Like the Search API, the Media Record API has fields that have been indexed and potentially modified by iDigBio. To identify the indexed fields available with the Media Record API, you can run the following:
media_fields_indexed <- idig_meta_fields(type = "media", subset = "indexed")
mfalli <- data.frame(matrix(ncol = 2, nrow = 0))
colnames(mfalli) <- c("Type", "FieldNameValue")
for(i in 1:length(media_fields_indexed)) {
mf <- data.frame(
Type = media_fields_indexed[[i]]$type,
FieldNameValue = media_fields_indexed[[i]]$fieldName,
stringsAsFactors = FALSE
)
mfalli <- rbind(mfalli, mf)
}
colnames(mfalli) <- c("type", "fieldName")
nrow(mfalli)## [1] 21Note, all index fields associated with the Media Record API are
returned by default with the idig_search_media()
function.
mfalli$fieldName## [1] "accessuri" "datemodified" "dqs" "etag"
## [5] "flags" "format" "hasSpecimen" "licenselogourl"
## [9] "mediatype" "modified" "recordids" "records"
## [13] "recordset" "rights" "tag" "type"
## [17] "uuid" "version" "webstatement" "xpixels"
## [21] "ypixels"Retain records with these fields
To obtain records with these fields with the
idig_search_media() function, you simply list the
fields argument as equal to these fields.
out <- idig_search_media(rq=list(scientificname="Galax urceolata"),
fields = mfalli$fieldName)
out %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed"),
font_size = 12,
fixed_thead = T) %>%
scroll_box(width = "100%", height = "400px")| accessuri | datemodified | dqs | etag | flags | format | hasSpecimen | licenselogourl | mediatype | modified | recordids | records | recordset | rights | tag | type | uuid | version | webstatement | xpixels | ypixels |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| https://sernecportal.org/imglib/seinet/sernec/AASU/AASU003/AASU003140.JPG | 2023-09-19T18:27:27.369136+00:00 | 0.5454545 | 2751bcef86d28c336ec2288002976d7203ad65a1 | NULL | image/jpeg | TRUE | https://i.creativecommons.org/l/by-nc-sa/4.0/88x31.png | images | NA | urn:uuid:7d7d2427-c759-4de3-acd8-284b63940ad8 , 43c69d2a-0fd2-4d34-a1ef-50d0f9c01353://sernecportal.org/imglib/seinet/sernec/aasu/aasu003/aasu003140.jpg | 15e3814e-7cf8-47d4-97e7-24aa40169c85 | 43c69d2a-0fd2-4d34-a1ef-50d0f9c01353 | BY-NC-SA | NA | NA | 00cbc182-e2dc-42ca-b819-25dcd22d83d0 | NA | http://creativecommons.org/licenses/by-nc-sa/4.0/ | NA | NA |
| https://cdn.floridamuseum.ufl.edu/Herbarium/bc01d15f-54e9-4b2c-8bfe-7009dcb03a56 | 2023-05-05T10:24:14.261979+00:00 | 0.6363636 | fb4b642d8882a821b9cea56dbf6318c9bf9815e4 | NULL | image/jpeg | TRUE | https://i.creativecommons.org/l/by-nc/4.0/88x31.png | images | NA | 781fd581-7b93-471e-a025-413e4bcd849101d15f-54e9-4b2c-8bfe-7009dcb03a56 | df2b5e81-833f-4c65-849c-c3f5be0b2afd | 781fd581-7b93-471e-a025-413e4bcd8491 | BY-NC | NA | image | 0130f6e3-1a3c-4780-89c0-ec4e68b2e164 | NA | http://creativecommons.org/licenses/by-nc/4.0/ | NA | NA |
| https://sernecportal.org/imglib/seinet/sernec/CLEMS/CLEMS0042/CLEMS0042881.jpg | 2024-01-31T21:41:14.546463+00:00 | 0.5454545 | ba3d0b0ad5d427781a3cb1702e370908db6dbe80 | NULL | image/jpeg | TRUE | https://i.creativecommons.org/l/by-nc-sa/4.0/88x31.png | images | NA | 264c48ec-8636-451f-a7e0-74131bc6f84c://sernecportal.org/imglib/seinet/sernec/clems/clems0042/clems0042881.jpg, urn:uuid:9f976087-4ccd-4c57-b731-1b67f86fcbfe | e0cfd2ed-1e6c-4c7a-8634-a80e3a172886 | 264c48ec-8636-451f-a7e0-74131bc6f84c | BY-NC-SA | NA | NA | 0162e889-a0e4-443b-8d43-70f47bb9bc60 | NA | http://creativecommons.org/licenses/by-nc-sa/4.0/ | NA | NA |
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| https://cdn.floridamuseum.ufl.edu/Herbarium/5dcb2ba3-7e83-4f91-bb52-ba263bf86aaa | 2023-05-05T10:24:14.261979+00:00 | 0.6363636 | 90e254c34f2ae98d4aa1c3850a413749cd2d9eef | NULL | image/jpeg | TRUE | https://i.creativecommons.org/l/by-nc/4.0/88x31.png | images | NA | 781fd581-7b93-471e-a025-413e4bcd8491\5dcb2ba3-7e83-4f91-bb52-ba263bf86aaa | cdb1d275-8885-4c32-b625-06d7b3c0af9f | 781fd581-7b93-471e-a025-413e4bcd8491 | BY-NC | NA | image | 024810b0-60e3-4f0e-a533-341fb83c0477 | NA | http://creativecommons.org/licenses/by-nc/4.0/ | NA | NA |
| http://purl.dlib.indiana.edu/iudl/herbarium/full/IND-0096109 | 2023-08-24T21:46:34.393325+00:00 | 0.5454545 | a1cf53de93079126edd234915e45ef5d32d2e587 | NULL | image/jpeg | TRUE | https://i.creativecommons.org/l/by-nc-sa/4.0/88x31.png | images | NA | urn:uuid:bf8b480a-0649-4848-b0b2-e656e2b38bcc , 0dab1fc7-ca99-456b-9985-76edbac003e0://purl.dlib.indiana.edu/iudl/herbarium/full/ind-0096109 | b3b8dd78-3437-407b-9e39-d517d443e4a7 | 0dab1fc7-ca99-456b-9985-76edbac003e0 | BY-NC-SA | NA | NA | 037146a5-aaf1-4d76-b1b3-48c65f5bf497 | NA | http://creativecommons.org/licenses/by-nc-sa/4.0/ | NA | NA |
| https://sernecportal.org/imglib/seinet/sernec/ETSU/ETSU025/ETSU025791.jpg | 2023-09-19T18:21:43.711409+00:00 | 0.5454545 | c8ff5fc834ef93be7ac401648042e854ef5f12d8 | NULL | image/jpeg | TRUE | https://i.creativecommons.org/l/by-nc-sa/4.0/88x31.png | images | NA | 21b563bc-70c2-46d5-bce8-2489db2db3d8://sernecportal.org/imglib/seinet/sernec/etsu/etsu025/etsu025791.jpg, urn:uuid:b7447460-5987-4627-90d0-a770c7e0f4d2 | 7a7f8c88-4949-4de9-b211-83c558fe6bab | 21b563bc-70c2-46d5-bce8-2489db2db3d8 | BY-NC-SA | NA | NA | 056fa51c-cab6-4f84-aae1-b58aef6557b5 | NA | http://creativecommons.org/licenses/by-nc-sa/4.0/ | NA | NA |
| https://sernecportal.org/imglib/seinet/sernec/DUKE/DUKE10095/DUKE10095615.jpg | 2024-05-14T20:32:32.494805+00:00 | 0.5454545 | a8e5beda9a8d4aa3abae043f7f04b8acba117238 | NULL | image/jpeg | TRUE | https://i.creativecommons.org/l/by-nc-sa/4.0/88x31.png | images | NA | 6258d160-a7aa-4937-bce3-3538eebd374f://sernecportal.org/imglib/seinet/sernec/duke/duke10095/duke10095615.jpg, urn:uuid:a21f18bf-7604-4b4f-86f2-04abe3b02458 | 2822bb8f-e07a-4e57-8f98-e94189ff6268 | 6258d160-a7aa-4937-bce3-3538eebd374f | BY-NC-SA | NA | NA | 06809816-84fe-4322-bc71-57c3444ca68c | NA | http://creativecommons.org/licenses/by-nc-sa/4.0/ | NA | NA |
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| https://sernecportal.org/imglib/seinet/sernec/NCU_VascularPlants/NCU00080/NCU00080598_01.JPG | 2024-01-31T21:23:33.638909+00:00 | 0.5454545 | 84a88c33027bb876fc2d0944c4a095eefced43d3 | NULL | image/jpeg | TRUE | https://i.creativecommons.org/l/by-nc-sa/4.0/88x31.png | images | NA | 4e3043a6-d48a-4a35-b5fb-f67d50cbc158://sernecportal.org/imglib/seinet/sernec/ncu_vascularplants/ncu00080/ncu00080598_01.jpg, urn:uuid:37d0aaea-37d7-4fcb-8887-cb95de6e327b | 490467c4-0e8f-4e29-961b-b60d08473717 | 4e3043a6-d48a-4a35-b5fb-f67d50cbc158 | BY-NC-SA | NA | NA | 08f38f15-aae4-49d8-8f86-328dee1b0d89 | NA | http://creativecommons.org/licenses/by-nc-sa/4.0/ | NA | NA |
| https://midwestherbaria.org/imglib/storage/portals/seinet/midwest/HUNT/HUNT-003/HUNT-003735_1502824558_lg.jpg | 2023-08-24T21:46:48.745959+00:00 | 0.5454545 | 8610a9a9842fba2e2221086ec1b4a39dd2175da5 | NULL | image/jpeg | TRUE | https://i.creativecommons.org/l/by-nc-sa/4.0/88x31.png | images | NA | 67893f3c-c409-41c6-a8f2-47956739a911://midwestherbaria.org/imglib/storage/portals/seinet/midwest/hunt/hunt-003/hunt-003735_1502824558_lg.jpg, 67893f3c-c409-41c6-a8f2-47956739a911://storage.idigbio.org/portals/seinet/midwest/hunt/hunt-003/hunt-003735_1502824558_lg.jpg , 67893f3c-c409-41c6-a8f2-47956739a911://storage.idigbio.org/portals/seinet/midwest/hunt/hunt-003/hunt-003735_1502824558_lg.jpg , urn:uuid:db4cabb5-448f-431f-9db1-08ed31b17c18 , 67893f3c-c409-41c6-a8f2-47956739a911://midwestherbaria.org/imglib/midwest/hunt/hunt-003/hunt-003735_1502824558_lg.jpg | 1135b055-ad82-48e8-b91f-143de8361e27 | 67893f3c-c409-41c6-a8f2-47956739a911 | BY-NC-SA | NA | NA | 08f4c43d-c3d2-48f5-9750-6944b2a519f8 | NA | http://creativecommons.org/licenses/by-nc-sa/4.0/ | NA | NA |
| http://n2t.net/ark:/65665/m3d0ad797b-a3b3-4897-a05c-da0d0ec9e036 | 2024-08-02T15:26:54.511943+00:00 | 0.5454545 | 6997f97e87c83fdcb1dcfc7fd261d905e9d9cb3e | NULL | image/jpeg | TRUE | NA | images | NA | a6eee223-cf3b-4079-8bb2-b77dad8cae9d://collections.nmnh.si.edu/media/?i=10357438 | 29b3c295-42e1-4b49-b13b-6b8e63b1fac8 | a6eee223-cf3b-4079-8bb2-b77dad8cae9d | NA | NA | image | 0986b79d-171a-4591-89dc-be139a1889d2 | NA | NA | 2400 | 3600 |
| https://cdn.floridamuseum.ufl.edu/Herbarium/38e1cd80-05c2-445a-acb5-511f89a1a6a5 | 2023-05-05T10:24:14.261979+00:00 | 0.6363636 | c1d924175b6b44f3893a4827024146a07eda03cd | NULL | image/jpeg | TRUE | https://i.creativecommons.org/l/by-nc/4.0/88x31.png | images | NA | 781fd581-7b93-471e-a025-413e4bcd8491\38e1cd80-05c2-445a-acb5-511f89a1a6a5 | 640a9ab7-9e95-4ebb-a3c3-1a3c59b14eba | 781fd581-7b93-471e-a025-413e4bcd8491 | BY-NC | NA | image | 0986dd48-8c35-4ae6-be5d-68d60794615a | NA | http://creativecommons.org/licenses/by-nc/4.0/ | NA | NA |
| https://cyberfloralouisiana.com/images/LSUCollections/Vascular/NO/0/092/NO0092177_L.JPG | 2023-01-11T02:29:15.335943+00:00 | 0.4545455 | 0d383d4c885b086832321349a32e0dfc5b23553b | dwc_basisofrecord_invalid | image/jpeg | TRUE | https://i.creativecommons.org/l/by-nc-sa/4.0/88x31.png | images | NA | 4523e216-ee13-4b15-a3f7-a6fd56431604://cyberfloralouisiana.com/images/lsucollections/vascular/no/0/092/no0092177_l.jpg, urn:uuid:e8bda133-0e01-4b43-ac92-3033e0b10563 , 4523e216-ee13-4b15-a3f7-a6fd56431604://cyberfloralouisiana.com/images/lsucollections/vascular/no/0/092/no0092177_l.jpg | 0ff87b0c-c260-4349-b9c6-fb9e93e3e03e | 4523e216-ee13-4b15-a3f7-a6fd56431604 | BY-NC-SA | NA | NA | 09d96c75-2bba-4c70-9477-4f5b35dff7af | NA | http://creativecommons.org/licenses/by-nc-sa/4.0/ | NA | NA |
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