There are many fields that can be obtained via the Search and Media API. This tutorial is meant to aid in identifying these fields.
In this demo we will cover how to:
idig_meta_fields()idig_search_records()idig_meta_fields()idig_search_media()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.
## [1] FALSEHowever, they contain similar information. For example, scientificName can be found in both the raw and index fields.
## type fieldName
## 171 string data.dwc:scientificName## type fieldName
## 69 string scientificnameTo 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.
## [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"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 |
| https://herbarium.berry.edu/BCH-002464.jpg | 2023-09-19T18:26:48.295586+00:00 | 0.5454545 | 84707f99cd84f2513771f7145812936ac8e2d0d2 | NULL | image/jpeg | TRUE | https://i.creativecommons.org/l/by-nc-sa/4.0/88x31.png | images | NA | 33bac15d-b1d0-42a1-8801-86149887eeef://herbarium.berry.edu/bch-002464.jpg, 33bac15d-b1d0-42a1-8801-86149887eeef://herbarium.berry.edu/bch-002464.jpg , urn:uuid:3d74ba4a-79dd-49d4-bae2-4bb1e64c1102 | e8b647cd-2eed-42b3-8a7b-9c01910db703 | 33bac15d-b1d0-42a1-8801-86149887eeef | BY-NC-SA | NA | NA | 0a3928dc-ae96-4169-b8da-31f2db92fd11 | NA | http://creativecommons.org/licenses/by-nc-sa/4.0/ | NA | NA |
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