Digitization of historical dataset - Egypt Expedition

This dataset combines the benthic macrofaunal data obtained from the floristical and faunistical survey of A. Steuer in the coasts near Alexandria in 1933. The results of this expedition were published in 38 volumes between 1934 and 1940. In this study, we present the digitized data of 14 volumes concerning macrofaunal taxa (1935-1940). In rare cases, occurrence data for planktonic species were available in these volumes and were included in the digitized datasets.

The datasets were digitized by the LifeWatchGreece data management team. Irini Tsikopoulou (data manager), Stamatina Nikolopoulou (data, database and webgis application manager) and Aglaia Legaki (data manager) were the resource creators, Panagiotis D. Dimitriou (data manager) and Evangelia Avramidou (data manager) were content providers. Nicolas Bailly has checked difficult taxonomic cases.

The original data were collected by Dr. Adolf Steuer, professor at the University of Innsbruck, who organized and led the sampling expedition to the coasts near Alexandria, Egypt. After sampling, all collected specimens were preserved and sent to several experts for taxonomic identification. Each expert was responsible for the publication of his macrofaunal report.

The study area of the Egypt Expedition is located between the Western and Eastern harbors of Alexandria, including nearby localities such as Abukir Bay, the Suez Canal and the lakes Edku and Mariout (Fig. 1). The majority of the sampling stations do not exceed the isobath of 200 meter. The coasts that were investigated were in part shallow and sandy, in part steep. Information concerning the sediment characteristics and vegetation of the studied area was also available and included in the digitized dataset.

Figure 1.  

Stations as they were mapped in Steuer's preliminary report (1935).

Data rescue/digitization

The digitization of this historical dataset was supported by the LifeWatchGreece Research Infrastructure, funded by the Greek Government under the General Secretariat of Research and Technology (GSRT), ESFRI Projects, Structural Funds, OPCE II.

Regarding the Egypt expedition, the Egyptian Ministry of Finance funded the whole sampling campaign and provided Dr Steuer with the expedition vehicle of the Marine Laboratory of Alexandria, a 15 m long motor boat named “El Hoot”. Additionally, the Ministry of Finance provided access to the Marine Laboratory of Alexandria located within the harbor area of the Alexandria city, as well as a small row boat, an automobile and the sampling equipment.

Sampling took place at 172 locations in the marine area off Alexandria, in the Suez Canal, in the Nile river and in two lagoons (Lake Mariout and Lake Edku). Adolf Steuer was in charge of the sampling which lasted from April to November of 1933. A motor-launch (small military vessel) 15 m long, named "El Hoot", belonging to the Marine Laboratory, was used for the one-day trips at sea. Since it was difficult to sail too far from the shore, only two stations (station 26 and station 64) surpassed the 200 m isobath. In some cases a small rowing boat was also used. The collection of benthic samples was done almost exclusively by using a dredge with an opening of 20x70 cm. In only one case sampling was performed with a large otter trawl (bottom trawling) in the eastern part of Bay of Abukir, at a depth of 20 meters. A bottom sampler (Petersen's grab) of 0.2 m² surface was also used once in the Eastern harbor due to difficulties in its manipulation (Vatova 1935). In shallow water, where no other equipment could be used, the samples of benthos were taken by diving. The sites where the sampling was performed along the coast were: the mouth of the Nile near Rosetta (Rashid), Lake Mariout and Lake Edku. Concerning planktonic samples, vertical hauls were operated using a medium sized net with buckets of celluloid with a gauge bottom.

Every single dataset was digitized manually from scanned documents. Some publications were in French or in German, depending on the author, and therefore the information was translated to English. Species names and sampling location names in the digitized datasets were kept same as in the original paper. Afterwards, all scientific names were cross-checked and taxonomically updated using the Taxon Match tool of the World Register of Marine Species (WoRMS) (WoRMS Editorial Board 2016). Station coordinates were produced by georeferencing maps from Fauvel (1937) using a Geographic Information System (GIS). The digitized datasets are presented in a standardised way, using Darwin Core terminology, informations on taxonomy, locality, sampling date, sampling protocol and individual measurements where they were available.

Digitization process

The digitization of the historical publications concerning the Egypt Expedition is a challenging process due to their complexity and the variety of the format across the different faunistic reports. Information on the sampling protocol and the sampling sites were digitized mainly based on the preliminary reports of Steuer (1935) and Vatova (1935) enriched with information from maps and the main text in the rest of the publications. Occurrence data were digitized based on the individual faunistic reports. The data digitization was made using the Darwin Core terminology.

The digitization process of the Egypt Expedition datasets included several steps that are described below:

1. Data managers read and comprehended individual faunistic publications, in order to overcome difficulties originating from the heterogeneity in the format and the content among the historical papers. The original authors did not follow a specific format for the presentation of their results. Some of them included species distribution maps, some reported species list, sampling dates and depths, while others also recorded individual species counts. If there was a species list in the historical papers, species were recorded according to their taxonomical classification. Respectively, if there was a station list, stations were reported chronologically.
2. A spreadsheet was created for each faunistic report and were populated with original species names found at each location. In this stage of digitization process, obvious typographic errors were corrected. The spreadsheets also contained information on the sampling depth (minimum and maximum depth), sampling date (year, month, day), sampling protocol and habitat (substrate type and vegetation). For benthic samples, station depth and sampling depth were matched. In some faunistic reports, station depths were given in fathoms (i.e. approximately 1.8 meters). In these cases, station depths in the datasets were converted to meters. For some taxonomic groups, additional information such as sex, lifestage, individual counts or body length measurements were available, either on a species level or on a specimen level. Accepted taxon names and taxonomic classification, as derived from the World Register of Marine species, were also included in the spreadsheets.
3. After the digitization of all available information contained in the main text and tables in the publications, sampling stations were georeferenced using the species distribution maps in every faunistic report. Since there were no stations coordinates, latitude, longitude and coordinates uncertainty were estimated using a GIS based on the distribution maps in each publication and in Fauvel (1937). In cases, where a station was only referred to as a specific locality in the text, and not accompanied by a symbol on a map, a new station with higher uncertainty was created based on the locality description.
4. In the next step, a code (fieldNumber) was created for each sampling event. A unique event was defined as a sampling event that took place in a specific station at a specific time and sampling depth using a specific sampling protocol. In some cases several samples had been taken in a location without defining the sampling station but only the wider area. To represent these, a new station ID was created, accompanied by an respective location remark. A code (occurrenceID) was also created for each species occurrence record.
5. The outcome of the above digitization steps was twelve spreadsheets with 56 columns containing occurrence data of twelve benthic macrofaunal taxa. These tables were combined in the MedOBIS PostgreSQL database in order to correct mistakes originating from differences in the information or absence of information derived from Steuer's preliminary report (1935) and individual faunistic reports. In cases of corrections, original information was always kept as a remark in the dataset.
6. The final step was the publication of the data through the MedOBIS Data Repository (MedOBIS IPT - http://ipt.medobis.eu/) and the MedOBIS Geoportal (http://medobis.portal.lifewatchgreece.eu/viewer). The Integrated Publishing Toolkit (IPT) (Wieczorek and Braak 2015, http://www.gbif.org/ipt) is a free open source software tool and is used to publish and share biodiversity datasets through the GBIF network (http://www.gbif.org/). It uses Darwin Core (http://rs.tdwg.org/dwc/terms/) and Ecological Metadata Language (EML) standards. All datasets are distributed as Darwin Core Archives, a compressed file that contains: one or more data files with details for event, occurrence and measurements in a comma-separated or tab-separated list, an archive descriptor (meta.xml) file describing the individual data file columns used and a metadata file on EML describing the entire dataset. The datasets concerning different taxonomic groups were published separately with their metadata and individual URLs (Table 2). Since the repository does not currently support species measurements such as body and carapace length, this information is added in the supplementary files of the present paper (Suppl. material 1), following the recently developed Environmental data and Event schema of OBIS (De Pooter et al., in prep). The datasets are also available on MedOBIS Geoportal (a virtual lab on LifeWatchGreece Research Infrastructure), where all the taxonomic groups are visualized on a map. The Geoportal allows users to search and download marine species datasets from all over the Mediterranean in several different formats (CSV, KML, WFS, WMS). In addition, a MedOBIS mobile application has been developed on playstore (https://play.google.com/store/apps/details?id=com.Hcmr.LifeWatch).

Difficulties regarding data digitization

During the digitization process, several issues with the data were encountered. The majority of these problems were similar across datasets. In the following paragraphs, we will highlight the most common ones and explain how they have been dealt with.

1. Data on the same sampling event were scattered and repeated in different publications. This created inconsistencies both across and within publications. Information on stations characteristics and sampling protocol were often repeated with small differences, missings or typographic errors due to different languages in the publications as well as in the preliminary reports. Within each faunistic report, occurrence records were often presented in two different ways, once as a list of species by station and again as a list of stations by species, leading to small differences or typographic errors. For practical reasons, we decided to consider as correct the information on sampling protocol that was obtained from the preliminary reports and the information on species distribution obtained from species list rather than station list. In any case, different information was always kept as a remark in the datasets.
2. The final number of stations recorded was 172: a total of 150 benthic stations reported in the Steuer’s preliminary report (1935) enriched with 10 planktonic stations derived from the 12 faunistic reports and with 10 new stations generated during the digitization process. Some stations described only verbally in the faunistic reports were not on a map. For example, some species referred to be collected from the “eastern harbour, on the body of a ship” or “eastern harbour, epifauna” without displaying on the map. In such case, a new station was created (e.g. easterharbour1), in order to include all available information. Other examples were LacMarioutCenter and westernharbour1 stations. In addition, new station IDs had to be created by the data management team because some stations were reported in the historical maps without a station name. For example, a sampling position “near the bath” was mentioned and mapped in many reports without a specific station name. Other stations without a station name were coastAbuQir-nearRosetta, LakeEdku_marinebeach, LakeEdkubridge, offSidiBishr and Silsila.
3. Besides general difficulties, described above, some sampling stations needed extra consideration.
   • For station D2, the sampling date was not recorded in mollusks report (Steuer 1939b). Nevertheless, this gap was corrected using the 1st of October 1933 (1/10/1933) as the sampling date because all the trips were one day trips and in all papers D2 was visited only on that day.
   • Another problematic station was station 104. This station was reported in four faunistic reports: two of them without sampling date and the rest with different dates, 1/11/1933 in Sipuncula and 8/11/1933 in Polychaeta. Eventually, the date 8/11/1933 was considered as correct instead of 1/11/1933 and used for all the reports. This decision was made, because, as mentioned above, stations were reported in chronological order and station 104 was reported under the ones of 7/11 and before the ones of 9/11.
   • Some stations were reported with subdivisions. One of them was station 105 that was divided into 105a and 105b in some faunistic reports, but they were not mapped separately. In this case, we used the coordinates of station 105 with higher uncertainty for both subdivisions. In the report on mollusks, and specifically regarding the species Cerithium vulgatum and Tricolia pullus, the stations 105a and 105b were displayed on two maps in opposite locations (Steuer 1939b, figures 5 and 8 in pp.15 and 24).
   • Station 13 was also referred as 13b in the report on mollusks (Steuer 1939b) but it was mapped as station 13 and as a result we used the coordinates of station 13.
4. In some planktonic hauls it was difficult to distinguish sampling and station depth. For example, “…over about 15 fathoms 3 vertical hauls out of depths of 20 m” was the description of station plankton4a in the Sipuncula report (Steuer 1939a). Thus, it was assumed, in accordance with preliminary reports, that station depth was 15 fathoms (about 28 m) and sampling depth was 0-20 m.
5. In a few cases, specimens that were reported in the historical publications could not be taxonomically updated due to missing species name authorship or due to ambiguous names. For example, Heliacus moniliferus was recorded in the Mollusca report (Steuer 1939b), but actually this name is used for a fossil, not a living animal as reported in Steuer (1939b).
6. Original sampling date and sampling depth were not recorded in the historical papers concerning Echinodermata and Ascidiacea. During the digitization of all the datasets concerning the Egypt Expedition, it was clear that in most of the cases, sampling dates and sampling depths were the same as in other datasets of Egypt Expedition and as a result date and depth information were taken from other faunistic reports and the preliminary report.
7. Finally, maps were only available as a .pdf in the preliminary report so they were converted to a .jpg or .tiff, in order to proceed to integration in GIS and be georeferenced. Maps recorded the geographical information of the sampling stations. Maps were not ideally suited for georeferencing: they were not accurate, had no scale or map projection system, and the accuracy of the scanner which had created the digitized version was unknown. The original map had to be aligned with their actual geographical location, by linking each point to its equivalent on a modern, accurate digital map (Rumsey and Williams 2002). In the end, Geographic Coordinate System: GCS_WGS_1984 and Datum: D_WGS_1984 was defined as the geographical coordinate system for the maps and the stations were digitized in a new feature class in GIS on a scale of 1:250.000. However it is impossible to perfectly align old maps due to landscape changes over the decades. For example, both the harbor of Alexandria as well as Lake Mariout were significantly extended over the course of the 20th century. A coordinates uncertainty of around 200 meters was estimated by the root mean square (RMS) - this is the georeference error. This value describes how consistent the transformation is between the different control points. In some cases, where the sampling stations were not well defined on the maps (lack of station name, landscape changes) new points were placed on the map manually, with higher uncertainty. The planktonic stations were also placed manually on the map.

The Egypt expedition covered, with 162 benthic and 10 planktonic stations, the area along the coasts of Alexandria, the Suez Canal, the Nile river and the lakes Edku and Mariout (Fig. 2).

Figure 2.  

Georeferenced map of all stations from "The fishery grounds near Alexandria" macrofaunal reports.

31.054 and 31.473 Latitude; 30.426 and 29.658 Longitude.

This set of historical data includes distribution information for 571 marine macrobenthic species belonging to 10 phyla, 21 classes and 257 families (Fig. 3). Malacostraca was the most speciose class with 26% of total species found, followed by Polychaeta (21%), Gastropoda (20%) and Bivalvia (14%) (Fig. 4). The family with the highest number of species richness was Syllidae (17 species), followed by Trochidae (14 species) and Veneridae (11 species). For the rest of the families, more than half of them (146 of 257) were represented by a single species.

Figure 3.  

Percentage of macrofaunal species per phylum.

Figure 4.  

Number of macrofaunal species per class.

These macrofaunal species were distributed in 172 stations located in the marine area off Alexandria, Egypt (Table 2). Species richness at the different sampling stations was very heterogenous. The most species rich stations were station 61, located above the isobath of 50 fathoms (90m), station 35, off Sidi Bishr and station 7 located close to the Eastern Harbour of Alexandria. The ten most common species in the study area are presented in Table 3. These species were found in more than 10% of the total number of stations.